Proteins encoded by polynucleic acids of porcine reproductive and respiratory syndrome virus (PRRSV)

ABSTRACT

The present invention provides an isolated DNA sequence encoding, for example, at least one polypeptide selected from the group consisting of proteins encoded by one or more open reading frames (ORF&#39;s) of an Iowa strain of porcine reproductive and respiratory syndrome virus (PRRSV), specifically ISU-12, and the polypeptides encoded by the isolated DNA sequences. The present invention also concerns a vaccine comprising an effective amount of such a protein; methods of producing antibodies which specifically bind to such a protein; and methods of protecting a pig against a PRRSV, and treating a pig infected by a PRRSV.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention concerns polynucleic acids isolated from a porcine reproductive and respiratory syndrome virus (PRRSV), a protein and/or a polypeptide encoded by the polynucleic acids, a vaccine which protects pigs from a PRRSV based on the protein or polynucleic acids, methods of making the proteins, polypeptides and polynucleic acids, a method of protecting a pig from PRRS using the vaccine, a method of producing the vaccine, a method of treating a pig infected by or exposed to a PRRSV, and a method of detecting a PRRSV.

2. Discussion of the Background

Porcine reproductive and respiratory syndrome (PRRS), a new and severe disease in swine, was first reported in the U.S.A. in 1987, and was rapidly recognized in many western European countries (reviewed by Goyal, J. Vet. Diagn. Invest., 1993, 5:656-664; and in U.S. application Ser. Nos. 08/131,625 and 08/301,435). The disease is characterized by reproductive failure in sows and gilts, pneumonia in young growing pigs, and an increase in preweaning mortality (Wensvoort et al., Vet. Q., 13:121-130, 1991; Christianson et al., 1992, Am. J. Vet. Res. 53:485-488; U.S. application Ser. Nos. 08/131,625 and 08/301,435).

The causative agent of PRRS, porcine reproductive and respiratory syndrome virus (PRRSV), was identified first in Europe and then in the U.S.A. (Collins et al., 1992, J. Vet. Diagn. Invest., 4:117-126). The European strain of PRRSV, designated as Lelystad virus (LV), has been cloned and sequenced (Meulenberg et al., 1993, Virology, 192:62-72 and J. Gen. Virol., 74:1697-1701; Conzelmann et al., 1993, Virology, 193:329-339).

PRRSV was classified within a single genus arterivirus in the new virus family of Arteriviridae, which includes equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV) and simian hemorrhagic fever virus (SHFV) (Plagemann and Moennig, 1992, Adv. Virus. Res., 41:99-192; Godeny et al., 1993, Virology, 194:585-596; U.S. application Ser. Nos. 08/131,625, 08/301,435 and Cavanaugh D., 1997, Arch. Virol. 142:629-633). This group of single plus-strand RNA viruses shares many characteristics such as genome organization, replication strategy, morphology and macrophage tropism (Meulenberg et al., 1993; U.S. application Ser. Nos. 08/131,625 and 08/301,435). Subclinical infections and persistent viremia with concurrent antibody production are also characteristic histopathologic properties of the arteriviruses.

Antigenic, genetic and pathogenic variations have been reported among PRRSV isolates (Wensvoort et al., 1992, J. Vet. Diagn. Invest., 4:134-138; Mardassi et al., 1994, J. Gen. Virol., 75:681-685; U.S. application Ser. Nos. 08/131,625 and 08/301,435). Furthermore, U.S. and European PRRSV represent two distinct genotypes (U.S. application Ser. Nos. 08/131,625 and 08/301,435). Antigenic variability also exists among different North American isolates as well (Wensvoort et al., 1992). Marked differences in pathogenicity have been demonstrated not only between U.S. and European isolates, but also among different U.S. isolates (U.S. application Ser. Nos. 08/131,625 and 08/301,435).

The genomic organization of arteriviruses resembles coronaviruses and toroviruses in that their replication involves the formation of a 3′-coterminal nested set of subgenomic mRNAs (sg mRNAs) (Chen et al., 1993, J. Gen. Virol. 74:643-660; Den Boon et al., 1990, J. Virol., 65:2910-2920; De Vries et al., 1990, Nucleic Acids Res., 18:3241-3247; Kuo et al., 1991, J. Virol., 65:5118-5123; Kuo et al., 1992; U.S. application Ser. Nos. 08/131,625 and 08/301,435). Partial sequences of several North American isolates have also been determined (U.S. application Ser. Nos. 08/131,625 and 08/301,435; Mardassi et al., 1994, J. Gen. Virol., 75:681-685).

The genome of PRRSV is polyadenylated, about 15 kb in length and contains eight open reading frames (ORFs; Meulenberg et al., 1993; U.S. application Ser. Nos. 08/131,625 and 08/301,435). ORFs 1a and 1b probably encode viral RNA polymerase (Meulenberg et al., 1993). ORFs 5, 6 and 7 were found to encode a glycosylated membrane protein (E), an unglycosylated membrane protein (M) and a nucleocapsid protein (N), respectively (Meulenberg et al., 1995). ORFs 2 to 4 appear to have the characteristics of membrane-associated proteins (Meulenberg et al., 1993; U.S. application Ser. No. 08/301,435). The ORFs 2 to 4 of LV encode virion-associated proteins designated as GP₂, GP₃ and GP₄, respectively (Van Nieuwstadt et al, 1996, 70:4767-4772).

The major envelope glycoprotein of EAV encoded by ORF 5 may be the virus attachment protein, and neutralizing monoclonal antibodies (MAbs) are directed to this protein (de Vries, J. Virol. 1992; 66:6294-6303; Faaberg, J. Virol. 1995; 69:613-617). The primary envelope glycoprotein of LDV, a closely related member of PRRSV, is also encoded by ORF 5, and several different neutralizing MAbs were found to specifically immunoprecipitate the ORF 5 protein (Cafruny et al., Vir. Res., 1986; 5:357-375). Therefore, it is likely that the major envelope protein of PRRSV encoded by ORF 5 may induce neutralizing antibodies against PRRSV.

Several hypervariable regions within the ORF5 were identified and were predicted to be antigenic (U.S. application Ser. Nos. 08/131,625 and 08/301,435). It has been proposed that antigenic variation of viruses is the result of direct selection of variants by the host immune responses (reviewed by Domingo et al., J. Gen. Virol. 1993, 74:2039-2045). Thus, these hypervariable regions are likely due to the host immune selection pressure and may explain the observed antigenic diversity among PRRSV isolates.

The M and N proteins of U.S. PRRSV isolates, including ISU 3927, are highly conserved (U.S. application Ser. No. 08/301,435). The M and N proteins are integral to preserving the structure of PRRSV virions, and the N protein may be under strict functional constraints. Therefore, it is unlikely either that (a) the M and N proteins are subjected to major antibody selection pressure or that (b) ORFs 6 and 7, which are likely to encode the M and N proteins, are responsible for or correlated to viral virulence. Interestingly, however, higher sequence variation of the LDV M protein was observed between LDV isolates with differing neurovirulence (Kuo et al., 1992, Vir. Res. 23:55-72).

ORFs 1a and 1b are predicted to translate into a single protein (viral polymerase) by frameshifting. ORFs 2 to 6 may encode the viral membrane associated proteins.

In addition to the genomic RNA, many animal viruses produce one or more sg mRNA species to allow expression of viral genes in a regulated fashion. In cells infected with PRRSV, seven species of virus-specific mRNAs representing a 3′-coterminal nested set are synthesized (mRNAs 1 to 7, in decreasing order of size). mRNA 1 represents the genomic mRNA. Each of the sg mRNAs contains a leader sequence derived from the 5′-end of the viral genome.

The numbers of the sg mRNAs differ among arteriviruses and even among different isolates of the same virus. A nested set of 6 sg mRNAs was detected in EAV-infected cells and European PRRSV-infected cells. However, a nested set of six (LDV-C) or seven (LDV-P) sg mRNAs, in addition to the genomic RNA, is present in LDV-infected cells. The additional sg mRNA 1-1 of LDV-P contains the 3′-end of ORF 1b and can potentially be translated to a protein which represents the C-terminal end of the viral polymerase. Sequence analysis of the sg mRNAs of LDV and EAV indicates that the leader-mRNA junction motif is conserved. Recently, the leader-mRNA junction sequences of the European LV were also shown to contain a common motif, UCAACC, or a highly similar sequence.

The sg mRNAs have been shown to be packaged into the virions in some coronaviruses, such as bovine coronavirus (BCV) and transmissible gastroenteritis virus (TGEV). However, only trace amounts of the sg mRNAs were detected in purified virions of mouse hepatitis virus (MHV), another coronavirus. The sg mRNAs of LDV, a closely related member of PRRSV, are also not packaged in the virions, and only the genomic RNA was detected in purified LDV virions.

The sg mRNAs of LDV and EAV have been characterized in detail. However, information regarding the sg mRNAs of PRRSV strains, especially the U.S. PRRSV, is very limited. Thus, a need is felt for a more thorough molecular characterization of the sg mRNAs of U.S. PRRSV.

The packaging signal of MHV is located in the 3′-end of ORF 1b, thus only the genomic RNA of MHV is packaged. The sg mRNAs of BCV and TGEV, however, are found in purified virions. The packaging signal of BCV and TGEV has not been determined. The Aura alphavirus sg mRNA is efficiently packaged into the virions, presumably because the packaging signal is present in the sg mRNA. The sindbis virus 26S sg mRNA is not packaged into virions because the packaging signal is located in the genome segment (not present in sg mRNA).

Several mechanisms are involved in the generation of the sg mRNAs. It has been proposed that coronaviruses utilize a unique leader RNA-primed transcription mechanism in which a leader RNA is transcribed from the 3′ end of the genome-sized negative-stranded template RNA, dissociates from the template, and then rejoins the template RNA at downstream intergenic regions to prime the transcription of sg mRNAs. The model predicts that the 5′-leader contains a specific sequence at its 3′-end which is repeated further downstream in the genome, preceding each of the ORFs 2 to 7. The leader joins to the body of each of the sg mRNAs via the leader-mRNA junction segment.

The various strains of PRRSV continue to be characterized (Halbur et al., J. Vet. Diagn. Invest. 8:11-20 (1996); Meng et al., J. Vet. Diagn. Invest. 8:374-381 (1996); Meng et al., J. Gen. Virol. 77:1265-1270 (1996); Meng et al., J. Gen. Virol. 76:3181-3188 (1995); Meng et al., Arch. Virol. 140:745-755 (1995); Halbur et al., Vet. Pathol. 32:200-204 (1995); Morozov et al., Arch. Virol. 140:1313-1319 (1995); Meng et al., J. Gen Virol. 75:1795-1801 (1994); Halbur et al., J. Vet. Diagn. Invest. 6:254-257 (1994), all of which are incorporated herein by reference in their entireties.)

PRRSV is an important cause of pneumonia in nursery and weaned pigs. PRRSV causes significant economic losses from pneumonia in nursery pigs (the exact extent of which are not fully known). Reproductive disease was the predominant clinical outcome of PRRSV infections during the past few years, due to the early prevalence of relatively low virulence strains of PRRSV. Respiratory disease has now become the main problem associated with PRRSV, due to the increasing prevalence of relatively high virulence strains of PRRSV. A need is felt for a vaccine to protect against disease caused by the various strains of PRRSV.

Surprisingly, the market for animal vaccines in the U.S. and worldwide is larger than the market for human vaccines. Thus, there exists an economic incentive to develop new veterinary vaccines, in addition to the substantial public health benefit which is derived from protecting farm animals from disease.

SUMMARY OF THE INVENTION

Accordingly, it is an object of the present invention to provide a DNA sequence encoding a porcine reproductive and respiratory syndrome virus (PRRSV) which contains SEQ ID NO: ______ (ISU-12) or SEQ ID NO: ______ (ISU-55).

It is another object of the invention to provide a DNA sequence encoding an open reading frame of ISU-12 including nucleotides 191-7387 of SEQ ID NO:______ (ORF1a), nucleotides 7375-11757 of SEQ ID NO: ______ (ORF 1b), nucleotides 11762-12529 of SEQ ID NO:______ (ORF 2), nucleotides 12385-13116 of SEQ ID NO:______ (ORF 3), nucleotides 12930-13463 of SEQ ID NO:______ (ORF 4), nucleotides 13477-14076 of SEQ ID NO:______ (ORF 5), nucleotides 1467-14585 of SEQ ID NO: ______ (ORF 6) and nucleotides 14578-14946 of SEQ ID NO: ______ (ORF 7);

-   -   or of ISU-55 of ISU-12 including nucleotides 191-7699 of SEQ ID         NO:______ (ORF1a), nucleotides 7657-12009 of SEQ ID NO:______         (ORF 1b), nucleotides 12074-12841 of SEQ ID NO:______ (ORF 2),         nucleotides 12697-13458 of SEQ ID NO:______ (ORF 3), nucleotides         13242-13775 of SEQ ID NO:______ (ORF 4), nucleotides 13789-14388         of SEQ ID NO:______ (ORF 5), nucleotides 14376-14897 of SEQ ID         NO:______ (ORF 6) and nucleotides 14890-15258 of SEQ ID         NO:______ (ORF 7).

It is also an object of the invention to provide a polypeptide encoded by the DNA sequence encoding ISU-12 or ISU-55, or one or more ORFs thereof.

Yet another object of the invention is to provide a composition for inducing antibodies against PRRSV comprising one or more polypeptides encoded by the DNA sequences of one or more ORF of ISU-12 or ISU-55.

Another object of the invention is to provide a method of protecting a pig from a porcine reproductive and respiratory disease, by administering an effective amount of the polypeptides encoded by the DNA sequences of one or more ORFs of ISU-12 or ISU-55 to a pig in need of protection against said disease.

It is yet another object of the invention to provide a method of distinguishing PRRSV strain ISU-55 from other strains of PRRSV by:

(a) amplifying a DNA sequence of the PRRSV using the following two primers: 55F 5′-CGTACGGCGATAGGGACACC-3′ and 3RFLP 5′-GGCATATATCATCACTGGCG-3′;

-   -   (b) digesting the amplified sequence of step (a) with DraI; and     -   (c) correlating the presence of three restriction fragments of         626 bp, 187 bp and 135 bp with a PRRSV ISU-55 strain.

These and other objects, which will become apparent during the following description of the preferred embodiments, have been provided by a purified and/or isolated polypeptide selected from the group consisting of proteins encoded by one or more open reading frames (ORF's) of an Iowa strain of porcine reproductive and respiratory syndrome virus (PRRSV), proteins at least 94% but less than 100% homologous with a protein encoded by an ORF 2 of an Iowa strain of PRRSV, proteins at least 88% but less than 100% homologous with a protein encoded by ORF 3 of an Iowa strain of PRRSV, proteins at least 93% homologous with an ORF 4 of an Iowa strain of PRRSV, proteins at least 90% homologous with an ORF 5 of an Iowa strain of PRRSV, proteins at least 97% but less than 100% homologous with proteins encoded by one or both of ORF 6 and ORF 7 of an Iowa strain of PRRSV, antigenic regions of such proteins which are at least 5 amino acids in length and which effectively stimulate protection in a porcine host against a subsequent challenge with a PRRSV isolate, and combinations thereof; an isolated polynucleic acid which encodes such a polypeptide or polypeptides; a vaccine comprising an effective amount of such a polynucleotide or polypeptide(s); antibodies which specifically bind to such a polynucleotide or polypeptide; methods of producing the same; and methods of (i) effectively protecting a pig against PRRS, (ii) treating a pig exposed to a PRRSV or suffering from PRRS, and (iii) detecting a PRRSV using the same.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A, 1B, 1C, 1D, 1E, 1F and 1G shows a nucleotide sequence comparison of ORFs 2 to 5 of U.S. isolates ISU 79, ISU 1894, ISU 3927, ISU 22 and ISU 55 with other known PRRSV isolates;

FIGS. 2A, 2B, 2C and 2D respectively show the alignment of the deduced amino acid sequences of ORF 2, ORF 3, ORF 4 and ORF 5 of U.S. isolates ISU 79, ISU 1894, ISU 22, ISU 55 and ISU 3927 with other known PRRSV isolates;

FIG. 3 shows a phylogenetic tree based on the nucleotide sequences of ORFs 2 to 7 of seven U.S. PRRSV isolates with differing virulence;

FIG. 4 shows a Northern blot analysis of RNAs isolated from ISU 3927-infected CRL 11171 cells (lane 1) and from purified virions of ISU 3927 (lane 2);

FIG. 5 shows a Northern blot analysis of total intracellular RNAs isolated from CRL 11171 cells infected with ISU22 (lane 1), ISU 55 (lane 2), ISU 79 (lane 3), ISU 1894 (lane 4) and ISU 3927 (lane 5), respectively;

FIGS. 6A and 6B show a Northern hybridization of total RNAs isolated from CRL 11171 cells infected with ISU 79 at different multiplicities of infection (m.o.i.) (A), and polyadenylated RNA from cells infected with PRRSV isolates ISU 55 and ISU 79 (B);

FIGS. 7A and 7B show a Northern blot analysis of total intracellular mRNAs isolated from CRL 11171 cells infected with ISU 1894 (A) and ISU 79 (B);

FIGS. 8A and 8B show RT-PCR amplification of the 5′-terminal sequences of the sg mRNAs 3 and 4 of ISU 1894 (lane 1) and sg mRNAs 3, 4 and 4-1 of ISU 79 (lane 2) (A) where lane L is a 1-kb marker; and the leader-mRNA junction sequences of sg mRNAs 3 and 4 of ISU 79 and ISU 1894 and of sg mRNA 4-1 of ISU 79 (B), where the locations of the leader-mRNA junction sequences in the genomes relative to the start codon of each ORF were indicated by minus (−) numbers of nucleotides upstream of the ORFs.

FIGS. 9A, 9B, 9C and 9D shows the sequence alignment of ORFs 2 to 7 of ISU 1894 and ISU 79, where the start codon of each ORF is indicated by +>, the termination codon of each ORF is indicated by asterisks (*), the determined or predicted leader-mRNA junction sequences are underlined and the locations of the leader-mRNA junction sequences relative to the start codon of each ORF are indicated by minus (−) numbers of nucleotides upstream of each ORF.

FIG. 10. Immunofluorescence assay of the MAbs with PRRSV-infected cells. Hybridoma supernatant was tested with IFA on infected ATCC CRL 11171 cells. Typical immunofluorescence from reaction with protein-specific MAbs is shown here. A. GP4-specific MAb, PP4bB3; B. E-specific MAb, PP5 dB4; C. N-specific MAb, PPeFl1; and D. Negative control, PPAc8.

FIG. 11. Reactivity of the MAbs and detergent extracted PRRSV antigen in ELISA. Plates were coated with antigen extracted from PRRSV-infected cells with detergent 1% Triton X-100 and blocked with 1% BSA. Hybridoma supernatant was tested along with positive and negative controls, PPeFl1 and PPAc8 respectively. Specific reactions were detected with anti-mouse IgG peroxidase conjugate. ABTS substrate was incubated in the plates for 20 min before A405 was measured. The first four MAbs starting from PP4bB3 are GP4-specific antibodies, and the next six MAbs starting from PP5bH4 are E-specific antibodies.

FIG. 12. Reactivity of the E specific MAbs and extract of PRRSV virions in Immunoblotting. MW standards (in kDa) are indicated on the left side of the figure. Lanes: 1, PP5 dB4; 2, PP5bH4; 3, Negative control: PPAc8; 4, Positive control: pig anti-PRRSV serum; 5, Negative control: normal pig serum.

FIG. 13. Titers of monoclonal antibodies.

FIG. 14. Reactivity pattern of PRRSSV isolates with the MAbs to PRRSV. Titers of the MAbs were shown in FIG. 13. The reactivity pattern was determined according to the titers of at least 6 MAbs with any one isolate: <=32—low reactivity; 64 to 128—medium reactivity; >=256—high reactivity. Those isolates not belonging to the groups above were grouped as other. Total isolates tested were 23.

FIG. 15. Immunofluorescence detection of recombinant protein expression in insect cells. The High Five™ cells were infected with vAc-P2 (A), vAc-P3 (B), vAc-P4 (C) and wt AcMNPV (D), fixed with methanol and reacted with pig anti-PRRSV serum. Specific reactions were detected by fluorescein-labeled goat anti-pig IgG conjugate and observed under fluorescence microscope.

FIG. 16. Cell surface expression of recombinant proteins in High Five™ cells. The insect cells were inoculated with vAc-P5 (A), vAc-M (B), vAc-N(C) and wt AcMNPV (D), incubated for 72 hrs, and stained at 4° C. without fixation and permeabilization. Pig anti-PRRSV serum was used to react with cell surface recombinant proteins and fluorescein-labeled goat anti-pig IgG conjugate was utilized to detect any specific reactions, which was observed under fluorescence microscope.

FIG. 17. Immunofluorescence detection of recombinant GP2, GP3 and GP4 proteins expressed in insect cells. The High Five™ cells were infected with recombinant baculovirus vAc-P2 containing ORF 2 (A), vAc-P3 containing ORF 3 (B), vAc-P4 containing ORF 4 (C) or wt AcMNPV (D), fixed with methanol and reacted with pig anti-PRRSV serum. Specific reactions were detected by fluorescein-labeled goat anti-pig IgG conjugate and observed under fluorescence microscope.

FIG. 18. Immunofluorescence detection of recombinant protein GP5, M and N expression in insect cells. The High Five™ cells were infected with recombinant baculovirus vAc-P5 containing ORF 5 (A), vAc-M containing the M gene (B), vAc-N containing the N gene (C) or wt AcMNPV (D), fixed with methanol and reacted with pig anti-PRRSV serum. Immunofluorescence is present in the cytoplasm in cells expressing E, M and N proteins.

FIG. 19. Immunoblotting detection of recombinant protein expression in insect cells. Whole protein was separated in 15% gel in SDS-PAGE and transferred to nitrocellulose membrane. Pig anti-PRRSV serum was used to incubate the membrane and specific reactions were detected by goat anti-pig IgG peroxidase conjugate. MW standards (in kDa) are indicated on the left side of the figure. Lanes: 1. wt AcMNPV infected High Five™ cells; 2, vAc-P2 infected High Five™ cells; 3. vAc-P3 infected High Five™ cells; 4, vAc-P4 infected High Five™ cells; 5, purified PRRSV virions; 6, normal ATCC CRL 11171 cells. (B). Lanes: 1, vAc-P5 infected High Five™ cells; 2, wt AcMNPV infected High Five™ cells; 3, vAc-M infected High Five™ cells; 4, vAc-N infected High Five™ cells; 5, purified PRRSV virus; 6, normal ATCC CRL 11171 cells. The arrows indicate the positions or ranges in M, of recombinant proteins. The images were scanned with Hewlett Packard ScanJet 3c/T scanner and program of Adobe Photoshop 3.0 (Adobe System Inc.).

FIG. 20. Glycosylation analysis of the recombinant proteins E, M and N expressed in insect cells. (A). Tunicamycin treatment of insect cells infected with vAc-P2, vAc-P3, vAc-P4 or wt AcMNPV. (B). Tunicamycin treatment of insect cells infected with vAc-P5, vAc-M, vAc-N or wt AcMNPV.

FIG. 21. Primers used to amplify PRRSV ORFs 2 through 7 genes with PCR. The underlined sequence within each primer indicates the unique restriction enzyme site that was introduced to facilitate subsequent cloning steps.

FIG. 22. Recombinant proteins of PRRSV ORFs 2 to 5 expressed in insect cells. a=predicted M_(r) of products of PRRSV ORFs 2 to 5 and N-glycosylation sites are based on nucleotide sequence studies (Meng et al, 1994 & Morozov et al, 1995). b=expressed products in inset cells. c=bands after tunicamycin treatment were determined by immunoblotting analysis. d=leader-free core proteins are determined on the basis of tunicamycin treatment analysis. the presence of the other bands in the recombinant products after tunicamycin treatment was possibly due to O-linked glycosylation, phosphorylation or other post-translational modifications.

FIG. 23 shows 20 overlapping cDNA clones sequenced from the VR 2385 cDNA library.

FIG. 24 shows the DNA alignment of the leader sequence of VR 2385 and LV.

FIG. 25 shows alignments of ORF1a of VR 2385 and LV. FIG. 25A shows the 5′ end alignment. FIG. 25B shows the middle DNA alignment. FIG. 25C shows the 3′ end alignment.

FIG. 26 shows the results of nested RT PCR with leader and ORF specific primers to amplify PCR products corresponding to mRNAs 4a, 5a and 7a.

FIG. 27 shows the DNA sequence alignment of low passage and high passage ISU-55.

FIG. 28 shows the ORF maps of ISU-55 high passage and low passage strains.

FIG. 29 is a restriction map showing the addition DraI site in the sequence of the high passage ISU-55 strain.

FIG. 30 shows the results of a RFLP test on total RNA isolated from ISU-55 hp, ISU-12 lp and ISU-12hp strains and used in RT PCR with primers 55F and 3RFLP.

FIG. 31 shows a genomic map and list of ORFs of ISU-55hp.

FIG. 32 shows the nucleotide sequence of ISU-55.

FIG. 33 shows the nucleotide sequence of ISU-12 (VR2385).

FIG. 34 shows the alignment of the nucleotide sequence of ISU-55 and ISU-12 (VR2385).

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

In the present application, the nucleotide sequences of the ORFs 2 to 5 of a low virulence isolate and four other Iowa strain PRRSV isolates with “moderate” and high virulence have been determined. Based on comparisons of ORFs 2 to 7 of various PRRSV isolates, the least virulent U.S. isolate known (ISU 3927) has relatively high sequence variations in ORFs 2 to 4, as compared to the variations in other U.S. isolates. Furthermore, based on analysis of the sequences of the ORFs, at least three minor genotypes exist within the major genotype of U.S. PRRSV.

Sequence analysis of the ORF 5 protein of different PRRSV isolates reveal three hypervariable regions which contained non-conserved amino acid substitutions. These regions are hydrophilic and also antigenic as predicted by computer analysis.

In the present invention, a “porcine reproductive and respiratory syndrome virus” or “PRRSV” refers to a virus which causes the diseases PRRS, PEARS, SIRS, MSD and/or PIP (the term “PIP” now appears to be disfavored), including the Iowa strain of PRRSV, other strains of PRRSV found in the United States (e.g., VR 2332), strains of PRRSV found in Canada (e.g., IAF-exp91), strains of PRRSV found in Europe (e.g., Lelystad virus, PRRSV-10), and closely-related variants of these viruses which may have appeared and which will appear in the future.

The “Iowa strain” of PRRSV includes (a) PRRSV isolates deposited in the American Type Culture Collection by the present inventors and/or described in this application and/or in either of prior U.S. application Ser. Nos. 08/131,625 and 08/301,435, (b) PRRS viruses which produce more than six sg mRNAs when cultured or passaged in CRL 11171 cells, (c) PRRSVs which produce at least 40% gross lung lesions or lung consolidation in 5-week-old caesarean-derived, colostrum-deprived piglets 10 days post-infection, (d) a PRRSV isolate having a genome which encodes a protein having the minimum homology to a PRRSV ORF described in Table 2 below, and/or (d) any PRRSV isolate having the identifying characteristics of such a virus.

The present vaccine is effective if it protects a pig against infection by a porcine reproductive and respiratory syndrome virus (PRRSV). A vaccine protects a pig against infection by a PRRSV if, after administration of the vaccine to one or more unaffected pigs, a subsequent challenge with a biologically pure virus isolate (e.g., VR 2385, VR 2386, or other virus isolate described below) results in a lessened severity of any gross or histopathological changes (e.g., lesions in the lung) and/or of symptoms of the disease, as compared to those changes or symptoms typically caused by the isolate in similar pigs which are unprotected (i.e., relative to an appropriate control). More particularly, the present vaccine may be shown to be effective by administering the vaccine to one or more suitable pigs in need thereof, then after an appropriate length of time (e.g., 1-4 weeks), challenging with a large sample (10³⁻⁷ TCID₅₀) of a biologically pure PRRSV isolate. A blood sample is then drawn from the challenged pig after about one week, and an attempt to isolate the virus from the blood sample is then performed (e.g., see the virus isolation procedure exemplified in Experiment VIII below). Isolation of the virus is an indication that the vaccine may not be effective, and failure to isolate the virus is an indication that the vaccine may be effective.

Thus, the effectiveness of the present vaccine may be evaluated quantitatively (i.e., a decrease in the percentage of consolidated lung tissue as compared to an appropriate control group) or qualitatively (e.g., isolation of PRRSV from blood, detection of PRRSV antigen in a lung, tonsil or lymph node tissue sample by an immunoperoxidase assay method [described below], etc.). The symptoms of the porcine reproductive and respiratory disease may be evaluated quantitatively (e.g., temperature/fever), semi-quantitatively (e.g., severity of respiratory distress [explained in detail below], or qualitatively (e.g., the presence or absence of one or more symptoms or a reduction in severity of one or more symptoms, such as cyanosis, pneumonia, heart and/or brain lesions, etc.).

An unaffected pig is a pig which has either not been exposed to a porcine reproductive and respiratory disease infectious agent, or which has been exposed to a porcine reproductive and respiratory disease infectious agent but is not showing symptoms of the disease. An affected pig is one which shows symptoms of PRRS or from which PRRSV can be isolated.

The clinical signs or symptoms of PRRS may include lethargy, respiratory distress, “thumping” (forced expiration), fevers, roughened haircoats, sneezing, coughing, eye edema and occasionally conjunctivitis. Lesions may include gross and/or microscopic lung lesions, myocarditis, lymphadenitis, encephalitis and rhinitis. In addition, less virulent and non-virulent forms of PRRSV and of the Iowa strain have been found, which may cause either a subset of the above symptoms or no symptoms at all. Less virulent and non-virulent forms of PRRSV can be used according to the present invention to provide protection against porcine reproductive and respiratory diseases nonetheless.

The phrase “polynucleic acid” refers to RNA or DNA, as well as mRNA and cDNA corresponding to or complementary to the RNA or DNA isolated from the virus or infectious agent. An “ORF” refers to an open reading frame, or polypeptide-encoding segment, isolated from a viral genome, including a PRRSV genome. In the present polynucleic acid, an ORF can be included in part (as a fragment) or in whole, and can overlap with the 5′- or 3′-sequence of an adjacent ORF (see for example, FIG. 1 and Experiment 1 below). A “polynucleotide” is equivalent to a polynucleic acid, but may define a distinct molecule or group of molecules (e.g., as a subset of a group of polynucleic acids).

In the Experiments described hereinbelow, the isolation, cloning and sequencing of ORFs 2 to 5 of (a) a low virulence U.S. PRRSV isolate and (b) two other U.S. PRRSV isolates of varying virulence were determined. The nucleotide and deduced amino acid sequences of these three U.S. isolates were compared with the corresponding sequences of other known PRRSV isolates (see, for example, U.S. application Ser. No. 08/301,435). The results indicate that considerable genetic variations exist not only between U.S. PRRSV and European PRRSV, but also among the U.S. isolates as well.

The amino acid sequence identity between the seven U.S. PRRSV isolates studied was 91-99% in ORF 2, 86-98% in ORF 3, 92-99% in ORF 4 and 88-97% in ORF 5. The least virulent U.S. isolate known (ISU 3927) has higher sequence variations in ORFs 2 to 4 than in ORFs 5 to 7, as compared to other U.S. isolates. Three hypervariable regions with antigenic potential have been identified in the major envelope glycoprotein encoded by ORF 5.

Pairwise comparison of the sequences of ORFs 2 to 7 and phylogenetic tree analysis implied the existence of at least three groups of PRRSV variants (or minor genotypes) within the major genotype of U.S. PRRSV. The least virulent U.S. isolate known forms a distinct branch from other U.S. isolates with differing virulence. The results of this study have implications for the taxonomy of PRRSV and vaccine development.

In a further experiment, the sg mRNAs in PRRSV-infected cells were characterized. The data showed that a 3′-coterminal nested set of six or seven sg mRNAs is formed in cells infected with different isolates of PRRSV. However, unlike some of the coronaviruses and alphavirus, the sg mRNAs of PRRSV are not packaged into the virion, and only was the genomic RNA of PRRSV detected in purified virions. Variations in the numbers of the sg mRNAs among different PRRSV isolates with differing virulence were also observed. Further sequence analysis of ORFs 2 to 7 of two U.S. isolates and their comparison with the European LV reveal the heterogeneic nature of the leader-mRNA junction sequences of PRRSV.

As demonstrated in Experiment 2 below, a 3′-coterminal nested set of six or more sg mRNAs is formed in cells infected with different isolates of PRRSV. The presence of a nested set of sg mRNAs further indicates that U.S. PRRSV, like the European isolate Lelystad virus (LV), belongs to the newly proposed Arteriviridae family including LDV, EAV and SHFV. Northern blot analysis with ORF-specific probes indicates that the structure of the PRRSV sg mRNAs is polycistronic, and each of the sg mRNAs except for sg mRNA 7 contains multiple ORFs. Therefore, the sequence of each sg mRNA is contained within the 3′-portion of the next larger sg mRNA, and not all 5′-ends of the sg mRNAs overlap with the sequences of the smaller sg mRNAs.

There is no apparent correlation, however, between the numbers of sg mRNAs and viral pneumovirulence. An additional species, sg mRNA 3-1, was found to contain a small ORF (ORF 3-1) with a coding capacity of 45 amino acids at its 5′-end.

In Experiment 2 below, the sg mRNAs of PRRSV are shown not to be packaged into the virions. Whether sg mRNAs are packaged into virions may depend an whether the sg mRNAs contain a packaging signal. Since the sg mRNAs of PRRSV are not packaged into virions, the encapsidation signal of PRRSV is likely localized in the ORF 1 region which is unique to the viral genome, but which is not present in the sg mRNAs.

In Experiment 2 below, the junction segments (the leader-mRNA junction sequences) of sg mRNAs 3 and 4 of two U.S. isolates of PRRSV, ISU 79 and ISU 1894, are determined. The knowledge of the leader-mRNA junction sequence identities provides means for effectively producing (a) chimeric viruses to be used as an infectious clone and/or as a vaccine, and (b) vectors for inserting or “shuttling” one or more genes into a suitable, infectable host. Methods for designing and producing such chimeric viruses, infectious clones and vectors are known (see, for example, Sambrook et al, “Molecular Cloning: A Laboratory Manual”, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.).

The leader-mRNA junction sequence of sg mRNAs 3 and 4 of the two isolates are different (TTGACC for mRNA 3-1 of ISU 79, GTAACC for mRNA 3, and TTCACC for mRNA 4). Most of the nucleotide differences in the junctions are present in the first 3 nucleotides. The last 3 nucleotides are invariable, suggesting that the joining of the leader sequence to the bodies of sg mRNAs occurs within the 5′-end of the leader-mRNA junction sequence. Similar observations have been reported for LV, EAV and LDV.

The acquisition of the additional sg mRNA 3-1 in isolate ISU 79 is due to a single nucleotide substitution which generates a new leader mRNA junction sequence. This substitution occurs in the last nucleotide of the junction segment, suggesting that the last nucleotide of the leader-mRNA junction motif is critical for the binding of the leader and for the initiation of transcription.

Although the sequence homology between the leader and the intergenic regions of coronaviruses led to the hypothesis that basepairing might be essential in the leader-primed transcription, no experimental evidence has documented for the requirement of base-pairing in transcription of the sg mRNAs. For example, the sequence at the 3′-end of the leader of both coronaviruses and arteriviruses that is involved in the fusion process remains unknown.

Several lines of evidence support the leader-primed transcription mechanism for coronaviruses, but the presence of negative-stranded sg mRNAs and sg replicative intermediates (sg RI) in coronavirus-infected cells suggests that the mechanism involved in sg mRNA synthesis is more complex than mere base-pairing of the leader sequence with a junction sequence. However, negative-stranded sg mRNAs have not been detected in arteriviruses except for LDV, and sg RIs have been detected only in EAV-infected cells. Therefore, sg mRNA synthesis in arteriviruses, and particularly in PRRSV, may be less complicated than in coronaviruses.

Sequence analysis of the ORFs 2 to 7 of two U.S. PRRSV isolates and comparison of the sequences with LV reveals the heterogeneity of the leader-mRNA junction sequences. The presence of the leader-mRNA junction motifs at positions which do not correspond to a sg mRNA raises a question as to whether the short stretch of only six nucleotides which are conserved in the leader and junction sequences in the genomes of PRRSV and other arteriviruses is sufficient for efficient binding of the leader to these specific junction sites upstream of the ORFs. This apparent discrepancy, however, may be explained by the following two possibilities.

First, additional structural elements, such as secondary structures or the sequences surrounding the leader-mRNA junction segment, are expected to be involved in the fusion (binding) of the leader to the specific sites. It has been shown that, in MHV, the sequence flanking the consensus sequence (leader-mRNA junction sequence) of UCUAAAC affects the efficiency of sg DI RNA transcription, and that the consensus sequence was necessary but not sufficient in and of itself for the synthesis of the DI mRNA.

Second, the distance between two leader-mRNA junction regions may affect the transcription of sg mRNAs. It has been demonstrated that the downstream leader-mRNA junction region was suppressing sg DI RNA synthesis of MHV from the upstream leader-mRNA junction region. The suppression was significant when the two leader-mRNA junction sequence separation was less than 35 nucleotides. However, significant inhibition of larger sg DI RNA synthesis (from the upstream leader-mRNA junction sequence) was not observed when the two leader-mRNA junction regions were separated by more than 100 nucleotides.

The previously reported experimental results are consistent with the observations reported in Experiment 2 below, where an additional species of sg mRNA 3-1, in addition to the sg mRNA 4, is observed in some of the PRRSV isolates. The leader-mRNA junction sequences of sg mRNAs 4 and 3-1 in the Iowa strain of PRRSV are separated by about 226 nucleotides. Therefore, the synthesis of the larger sg mRNA 3-1 from the upstream leader-mRNA junction sequence is not suppressed by the presence of the downstream leader-mRNA 4 junction sequence.

In contrast, multiple potential leader-mRNA junction sequences were found at different positions upstream of ORFs 3, 5, 6 and 7, but there were no sg mRNAs corresponding to these leader-mRNA junction motifs in the Northern blot analysis. Most of these leader-mRNA junction sequences are separated by less than 50 nucleotides from the downstream leader-mRNA junction region, except for ORF 7 (in which the two potential leader-mRNA junction sequences are separated by 114 nucleotides). However, sg mRNA 7 in Northern blot analysis showed a widely-diffused band. Therefore, transcription of the larger sg mRNA 7 from the upstream leader-mRNA junction sequence may not be significantly suppressed by the downstream junction sequence, but it is not easily distinguishable from the abundant sg mRNA 7 by Northern blot analysis.

The Present Polynucleotides and Polypeptides

ORF's 2-7 of plaque-purified PRRSV isolate ISU-12 (deposited on Oct. 30, 1992, in the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Md. 20852, U.S.A., under the accession numbers VR 2385 [3× plaque-purified] and VR 2386 [non-plaque-purified]) and ORF's 6-7 of PRRSV isolates ISU-22, ISU-55, ISU-3927 (deposited on Sep. 29, 1993, in the American Type Culture Collection under the accession numbers VR 2429, VR 2430 and VR 2431, respectively), ISU-79 and ISU-1894 (deposited on Aug. 31, 1994, in the American Type Culture Collection under the accession numbers VR 2474 and VR 2475, respectively) are described in detail in U.S. application Ser. No. 08/301,435. However, the techniques used to isolate, clone and sequence these genes can be also applied to the isolation, cloning and sequencing of the genomic polynucleic acids of any PRRSV. Thus, the present invention is not limited to the specific sequences disclosed in the Experiments below.

For example, primers for making relatively large amounts of DNA by the polymerase chain reaction (and if desired, for making RNA by transcription and/or protein by translation in accordance with known in vivo or in vitro methods) can be designed on the basis of sequence information where more than one sequence obtained from a PRRSV genome has been determined (e.g., ORF's 2-7 of VR 2385, VR 2429, VR 2430, VR 2431, VR 2474, ISU-1894, VR 2332 and Lelystad virus). A region from about 15 to 50 nucleotides in length having at least 80% and preferably at least 90% identity is selected from the determined sequences. A region where a deletion occurs in one of the sequences (e.g., of at least 5 nucleotides) can be used as the basis for preparing a selective primer for selective amplification of the polynucleic acid of one strain or type of PRRSV over another (e.g., for the differential diagnosis of North American and European PRRSV strains).

Once the genomic polynucleic acid is amplified and cloned into a suitable host by known methods, the clones can be screened with a probe designed on the basis of the sequence information disclosed herein. For example, a region of from about 50 to about 500 nucleotides in length is selected on the basis of either a high degree of identity (e.g., at least 90%) among two or more sequences (e.g., in ORF's 6-7 of the Iowa strains of PRRSV disclosed in Experiment III below), and a polynucleotide of suitable length and sequence identity can be prepared by known methods (such as automated synthesis, or restriction of a suitable fragment from a polynucleic acid containing the selected region, PCR amplification using primers which hybridize specifically to the polynucleotide, and isolation by electrophoresis). The polynucleotide may be labeled with, for example, ³²P (for radiometric identification) or biotin (for detection by fluorometry). The probe is then hybridized with the polynucleic acids of the clones and detected according to known methods.

The present Inventors have discovered that one or more of ORFs 2-4 may be related to the virulence of PRRSV. For example, at least one isolate of PRRSV which shows relatively low virulence also appears to have a deletion in ORF 4 (see, for example, Experiments VIII-XI in U.S. application Ser. No. 08/301,435). Furthermore, the least virulent known isolate (VR 2431) shows a relatively high degree of variance in both nucleotide and amino acid sequence information in ORFs 2-4, as compared to other U.S. PRRSV isolates. Thus, in one embodiment, the present invention concerns polynucleotides and polypeptides related to ORFs 2-4 of VR 2431.

In a further embodiment, the present invention is concerned with a polynucleic acid obtained from a PRRSV isolate which confers immunogenic protection directly or indirectly against a subsequent challenge with a PRRSV, but in which the polynucleic acid is deleted or mutated to an extent which would render a PRRSV containing the polynucleic acid either low-virulent (i.e., a “low virulence” (lv) phenotype; see the corresponding explanation in U.S. application Ser. No. 08/301,435) or non-virulent (a so-called “deletion mutant”). Preferably, one or more of ORFs 2-4 is/are deleted or mutated to an extent which would render a PRRS virus non-virulent. However, it may be desirable to retain regions of one or more of ORFs 2-4 in the present polynucleic acid which (i) encode an antigenic and/or immunoprotective peptide fragment and which (ii) do not confer virulence to a PRRS virus containing the polynucleic acid.

The present invention also encompasses a PRRSV per se in which one or more of ORFs 2-4 is deleted or mutated to an extent which renders it either low-virulent or non-virulent (e.g., VR 2431). Such a virus is useful as a vaccine or as a vector for transforming a suitable host (e.g., MA-104, PSP 36, CRL 11171, MARC-145 or porcine alveolar macrophage cells) with a heterologous gene. Preferred heterologous genes which may be expressed using the present deletion mutant may include those encoding a protein or an antigen other than a porcine reproductive and respiratory syndrome virus antigen (e.g., pseudorabies and/or swine influenza virus proteins and/or polypeptide-containing antigens, a porcine growth hormone, etc.) or a polypeptide-based adjuvant (such as those discussed in U.S. application Ser. No. 08/301,435 for a vaccine composition).

It may also be desirable in certain embodiments of the present polynucleic acid which contain, for example, the 3′-terminal region of a PRRSV ORF (e.g., from 200 to 700 nucleotides in length), at least part of which may overlap with the 5′-region of the ORF immediately downstream. Similarly, where the 3′-terminal region of an ORF may overlap with the 5′-terminal region of the immediate downstream ORF, it may be desirable to retain the 5′-region of the ORF which overlaps with the ORF immediately downstream.

The present inventors have also discovered that ORF 5 in the PRRSV genome appears to be related to replication of the virus in mammalian host cells capable of sustaining a culture while infected with PRRSV. Accordingly, the present invention is also concerned with polynucleic acids obtained from a PRRSV genome in which ORF 5 may be present in multiple copies (a so-called “overproduction mutant”). For example, the present polynucleic acid may contain at least two, and more preferably, from 2 to 10 copies of ORF 5 from a high-replication (hr) phenotype PRRSV isolate.

Interestingly, the PRRSV isolate ISU-12 has a surprisingly large number of potential start codons (ATG/AUG sequences) near the 5′-terminus of ORF 5, possibly indicating alternate start sites of this gene. Thus, alternate forms of the protein encoded by ORF 5 of a PRRSV isolate may exist, particularly where alternate ORF's encode a protein having a molecular weight similar to that determined experimentally (e.g., from about 150 to about 250 amino acids in length). The most likely coding region for ORF 5 of ISU-12 is indicated in FIG. 1.

One can prepare deletion and overproduction mutants in accordance with known methods. For example, one can prepare a mutant polynucleic acid which contains a “silent” or degenerate change in the sequence of a region encoding a polypeptide. By selecting and making an appropriate degenerate mutation, one can substitute a polynucleic acid sequence recognized by a known restriction enzyme (see, for example, Experiment 2 below). Thus, if a silent, degenerate mutation is made at one or two of the 3′-end of an ORF and the 5′-end of a downstream ORF, one can insert a synthetic polynucleic acid (a so-called “cassette”) which may contain a polynucleic acid encoding one or multiple copies of an hr ORF 5 protein product, of a PRRSV or other viral envelope protein and/or an antigenic fragment of a PRRSV protein. The “cassette” may be preceded by a suitable initiation codon (ATG), and may be suitably terminated with a termination codon at the 3′-end (TAA, TAG or TGA). Of course, an oligonucleotide sequence which does not encode a polypeptide may be inserted, or alternatively, no cassette may be inserted. By doing so, one may provide a so-called deletion mutant.

The present invention also concerns regions and positions of the polypeptides encoded by ORFs of VR 2431 which may be responsible for the low virulence of this isolate. Accordingly, the present isolated and/or purified polypeptide may be one or more encoded by a “low-virulence mutation” of one or more of ORFs 2, 3 and 4 of a PRRSV (or a low-virulence fragment thereof at least 5 amino acids in length) in which one or more of positions 12-14 of the polypeptide encoded by ORF 2 are RGV (in which “R”, “G” and “V” are the one-letter abbreviations for the corresponding amino acids), positions 44-46 are LPA, position 88 is A, position 92 is R, position 141 is G, position 183 is H, position 218 is S, position 240 is S and positions 252-256 are PSSSW, or any combination thereof. Other amino acid residue identities which can be further combined with one or more of the above amino acid position identities include those at position 174 (I) and position 235 (M).

The present isolated and/or purified polypeptide may also be one encoded by an ORF 3 of a PRRSV in which one or more of the specified amino acid identities may be selected from those at positions 11 (L), 23 (V), 26-28 (TDA), 65-66 (QI), 70 (N), 79 (N), 93 (T), 100-102 (KEV), 134 (K), 140 (N), 223-227 (RQRIS), 234 (A) and 235 (M), or any combination thereof, which may be further combined with one or more of positions 32 (F), 38 (M), 96 (P), 143 (L), 213-217 (FQTS), 231 (R), and 252 (A).

The present isolated and/or purified polypeptide may also be one encoded by an ORF 4 of a PRRSV in which one or more of the specified amino acid identities may be selected from those at positions 0.13 (E), 43 (N), 56 (G), 58-59 (TT), 134 (T), 139 (I) and any combination thereof, which may be further combined with one or more of positions 2-3 (AA), 51 (G) and 63 (P).

The present invention also concerns polynucleotide sequences encoding polypeptide sequences of 5 or more amino acids, preferably 10 or more amino acids, and up to the full length of the polypeptide, encoded by any one of ORFs 2-4 of VR 2431, in which the polynucleotides at the codon(s) corresponding to the amino acid positions detailed in the preceding three paragraphs are replaced with polynucleotides encoding the corresponding amino acids of the proteins encoded by the corresponding ORF of VR 2431.

In a further embodiment of the present invention, the polynucleic acid encodes one or more proteins, or antigenic regions thereof, of a PRRSV. Preferably, the present nucleic acid encodes at least one antigenic region of a PRRSV membrane (envelope) protein. More preferably, the present polynucleic acid encodes a hypervariable region from a ORF 5 PRRSV protein product (see the discussion below) or (b) contains at least one copy of the ORF-5 gene from a high virulence (hv) phenotype isolate of PRRSV (see the description of “hv phenotype” in U.S. application Ser. No. 08/301,435) and a sufficiently long fragment, region or sequence of at least one of ORF-2, ORF-3, ORF-4, ORF-5 and/or ORF-6 from the genome of a PRRSV isolate to encode an antigenic region of the corresponding protein(s) and effectively stimulate protection against a subsequent challenge with, for example, a hv phenotype PRRSV isolate.

Even more preferably, at least one entire envelope protein encoded by ORF-2, ORF-3, ORF-5 and/or ORF-6 of a PRRSV is contained in the present polynucleic acid, and the present polynucleic acid excludes or modifies a sufficiently long portion of one of ORFs 2-4 from a PRRSV to render a PRRSV containing the same either low-virulent or non-virulent. Most preferably, the polynucleic acid is isolated from the genome of an isolate of the Iowa strain of PRRSV (for example, VR 2385 (3× plaque-purified ISU-12), VR 2386 (non-plaque-purified ISU-12), VR 2428 (ISU-51), VR 2429 (ISU-22), VR 2430 (ISU-55), VR 2431 (ISU-3927), VR 2474 (ISU-79) and/or ISU-1894).

A further preferred embodiment of the present invention includes a polynucleotide encoding an amino acid sequence from a hypervariable region of ORF 5 of a PRRSV, preferably of an Iowa strain of PRRSV. Thus, such polynucleotides encode one (or more) of the following amino acid sequences: TABLE 1 Hypervariable Region 1 Hypervariable Region 2 Hypervariable Region 3 (positions 32-38) (Positions 57-66) (Pos'ns 120-128) NGNSGSN ANKFDWAVET LICFVIRLA SNDSSSH ANKFDWAVEP LTCFVIRFA SSSNSSH AGEFDWAVET LICFVIRFT SANSSSH ADKFDWAVEP LACFVIRFA HSNSSSH ADRFDWAVEP LTCFVIRFV SNSSSSH SSHFGWAVET LTCFIIRFA NNSSSSH FICFVIRFA NGGDSST(Y) FVCFVIRAA

In this embodiment, the polynucleotide may encode further amino acid sequences of a PRRSV ORF 5 (as disclosed in FIG. 3 or in U.S. application Ser. Nos. 08/131,625 or 08/301,435), as long as one or more of the hypervariable regions at positions 32-38, 57-66 and/or 120-128 are included. (The present invention specifically excludes the proteins and polynucleotides of ORF 5 of LV and VR 2332.)

A further preferred embodiment of the present invention concerns a purified preparation which may comprise, consist essentially of or consist of a polynucleic acid having a sequence of the formula (I) or (II): 5′-α-β-3′  (I) 5′-α-β-γ-3′  (II) wherein α encodes at least one polypeptide, or antigenic or low-virulence fragment thereof encoded by a polynucleotide selected from the group consisting of ORFs 2, 3 and 4 of an Iowa strain of PRRSV and regions thereof encoding such antigenic and/or low-virulence fragments; and β is at least one copy of an ORF 5 from an Iowa strain of PRRSV or an antigenic fragment thereof (e.g. one or more hypervariable regions), preferably a full-length copy from a high replication (hr) phenotype; and γ encodes at least one polypeptide or antigenic fragment thereof encoded by a polynucleotide selected from the group consisting of ORF 6 and ORF 7 of an Iowa strain of PRRSV and regions thereof encoding the antigenic fragments.

Alternatively, the present invention may concern a purified preparation which may comprise, consist essentially of or consist of a polynucleic acid having a sequence of the formula (III): 5′-β-δ-γ-3′  (III) where β and γ are as defined above; and δ is either a covalent bond or a linking polynucleic acid which does not materially affect transcription and/or translation of the polynucleic acid. Preferably, β is a polynucleotide encoding at least one hypervariable region of a protein encoded by an ORF 5 of an Iowa strain of PRRSV, and more preferably, encodes a full-length protein encoded by an ORF 5 of an Iowa strain of PRRSV.

The present invention may also concern a purified preparation which may comprise, consist essentially of or consist of a polynucleic acid having a sequence of the formula (IV): 5′-α-β-δ-γ-3′  (IV) where α, β, γ and δ are as defined in formulas (I)-(III) above.

The present invention may also concern a purified preparation which may comprise, consist essentially of or consist of a polynucleic acid, an expression vector or a plasmid having a sequence of the formula (V): 5′-ε-ζ-ι-κ-ξ-3′  (V) where ε, which is optionally present, is a 5′-terminal polynucleotide sequence which provides a means for operationally expressing the polynucleotides α, β, γ and δ; ζ is a polynucleotide of the formula KTVACC, where K is T, G or U, and V is A, G or C; ι is a polynucleotide of at most about 130 (preferably at most 100) nucleotides in length; κ is a polynucleotide comprising one or more genes selected from the group consisting of a conventional marker or reporter gene, α, β, γ, and operationally linked combinations thereof, where α, β, and γ are as defined in formulas (I)-(IV) above; and ξ, which is optionally present, is a 3′-terminal polynucleotide sequence which does not suppress the operational expression of the polynucleotides α, β, γ and δ, and which may be operationally linked to ε (for example, in a plasmid).

Suitable marker or reporter genes include, e.g., those providing resistance to an antibiotic such as neomycin, erythromycin or chloramphenicol; those encoding a known, detectable enzyme such as β-lactamase, DHFR, horseradish peroxidase, glucose-6-phosphate dehydrogenase, alkaline phosphatase, and enzymes disclosed in U.S. Pat. No. 4,190,496, col. 32, line 33 through col. 38, line 44 (incorporated herein by reference), etc.; and those encoding a known antibody (e.g., mouse IgG, rabbit IgG, rat IgG, etc.) or known antigenic protein such as Protein A, Protein G, bovine serum albumin (BSA), keyhole limpet hemocyanin (KLH), bovine gamma globulin (BGG), lactalbumin, polylysine, polyglutamate, lectin, etc.

The polynucleotide ι is preferably a polynucleotide sequence at least 80% homologous to a polynucleotide sequence from a PRRSV genome located between a leader-mRNA junction sequence and the start codon of the ORF immediately downstream. “About 130” nucleotides in length refers to a length of the polynucleotide ι which does not adversely affect the operational expression of κ. For example, in ISU 79, a leader-mRNA junction sequence which does not suppress expression of ORF 7 can be found 129 bases upstream from the start codon of ORF 7 (see Experiment 2 below). Suitable exemplary sequences for the polynucleotide ι can be deduced from the sequences shown in FIGS. 1 and 9.

The present polynucleic acid may also comprise, consist essentially of or consist of combinations of the above sequences, either as a mixture of polynucleotides or covalently linked in either a head-to-tail (sense-antisense) or head-to-head fashion. Polynucleic acids complementary to the above sequences and combinations thereof (antisense polynucleic acid) are also encompassed by the present invention. Thus, in addition to possessing multiple or variant copies of ORF 5, the present polynucleic acid may also contain multiple or variant copies of one or more of ORF's 1-7, including antigenic or hypervariable regions of ORF 5, of Iowa strain PRRSV's.

Similar to the methods described above and in the Experiments described below and in U.S. application Ser. Nos. 08/131,625 and 08/301,435, one can prepare a library of recombinant clones (e.g., using E. coli as a host) containing suitably prepared restriction fragments of a PRRSV genome (e.g., inserted into an appropriate plasmid expressible in the host). The clones are then screened with a suitable probe (e.g, based on a conserved sequence of ORF's 2-3; see, for example, FIG. 22 of U.S. application Ser. No. 08/301,435). Positive clones can then be selected and grown to an appropriate level. The polynucleic acids can then be isolated from the positive clones in accordance with known methods. A suitable primer for PCR can then be designed and prepared as described above to amplify the desired region of the polynucleic acid. The amplified polynucleic acid can then be isolated and sequenced by known methods.

The present purified preparation may also contain a polynucleic acid selected from the group consisting of sequences having at least 97% sequence identity (or homology) with at least one of ORFs 5-7 of VR 2385, VR 2430 and/or VR 2431; and sequences encoding a polypeptide having at least the minimum sequence identity (or homology) with at least one of ORF's 2-5 of VR 2385, VR 2428, VR 2429, VR 2430, VR 2431, VR 2474 and ISU-1894, as follows: TABLE 2 Minimum % Homology with ORF: Relative to Isolate: 2 3 4 5 VR 2385 99 92 95 90 VR 2429 100 99 99 98 VR 2430 98 95 96 90 VR 2431 94 88 93 92 VR 2474 99 97 97 95 ISU 1894 97 97 99 97

Preferably, the polynucleic acid excludes or modifies a sufficiently long region or portion of one or more of ORFs 24 of the hv PRRSV isolates VR 2385, VR 2429, ISU-28, ISU-79 and/or ISU-984 to render the isolate low-virulent or non-virulent.

In the context of the present application, “homology” refers to the percentage of identical nucleotide or amino acid residues in the sequences of two or more viruses, aligned in accordance with a conventional method for determining homology (e.g., the MACVECTOR or GENEWORKS computer programs, aligned in accordance with the procedure described in Experiment III in U.S. application Ser. No. 08/301,435).

Preferably, the present isolated polynucleic acid encodes a protein, polypeptide, or antigenic fragment thereof which is at least 10 amino acids in length and in which non-homologous amino acids which are non-essential for antigenicity may be conservatively substituted. An amino acid residue in a protein, polypeptide, or antigenic fragment thereof is conservatively substituted if it is replaced with a member of its polarity group as defined below:

Basic Amino Acids:

-   -   lysine (Lys), arginine (Arg), histidine (His)         Acidic Amino Acids:     -   aspartic acid (Asp), glutamic acid (Glu), asparagine (Asn),         glutamine (Gln)         Hydrophilic, Nonionic Amino Acids:     -   serine (Ser), threonine (Thr), cysteine (Cys), asparagine (Asn),         glutamine (Gln)         Sulfur-Containing Amino Acids:     -   cysteine (Cys), methionine (Met)         Hydrophobic, Aromatic Amino Acids:     -   phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp)         Hydrophobic, Nonaromatic Amino Acids:     -   glycine (Gly), alanine (Ala), valine (Val), leucine (Leu),         isoleucine (Ile), proline (Pro)

More particularly, the present polynucleic acid encodes one or more of the protein(s) encoded by the second, third, fourth, fifth, sixth and/or seventh open reading frames (ORF's 2-7) of the PRRSV isolates VR 2385, VR 2386, VR 2428, VR 2429, VR 2430, VR 2431, VR 2474 and/or ISU-1894 (e.g., one or more of the sequences shown in FIG. 3 and/or SEQ ID NOS:15, 17, 19, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63 and 65 of U.S. application Ser. No. 08/301,435).

ORF's 6 and 7 are not likely candidates for controlling virulence and replication phenotypes of PRRSV, as the nucleotide sequences of these genes are highly conserved among high virulence (hv) and low virulence (lv) isolates (see Experiment III of U.S. application Ser. No. 08/301,435). However, ORF 5 in PRRSV isolates appears to be less conserved among high replication (hr) and low replication (lr) isolates. Therefore, it is believed that the presence of an ORF 5 from an hr PRRSV isolate in the present polynucleic acid will enhance the production and expression of a recombinant vaccine produced from the polynucleic acid.

Furthermore, ORF 5 of PRRSV contains three hydrophilic, hypervariable regions typically associated with antigenicity in a polypeptide. Thus, the present invention also encompasses polynucleotides encoding a polypeptide comprising one or more hypervariable regions of a PRRSV ORF 5, preferably a polypeptide of the formula a-b-c-d-e-f-g, where:

-   -   a is an amino group, a poly(amino acid) corresponding to         positions 1-31 of a protein encoded by a PRSSV ORF 5, or a         fragment of such a poly(amino acid) which does not adversely         affect the antigenicity of the polypeptide;     -   b is an amino acid sequence selected from the group consisting         of those sequences listed under Hypervariable Region No. 1 in         Table 1 above,     -   c is an amino acid sequence corresponding to positions 39-56 of         a protein encoded by a PRSSV ORF 5 (preferably a sequence of the         formula LQLIYNLTLCELNGTDWL, in which one or more [preferably         1-10] amino acids may be conservatively substituted),     -   d is an amino acid sequence selected from the group consisting         of those sequences listed under Hypervariable Region No. 2 in         Table 1 above,     -   e is an amino acid sequence corresponding to positions 67-119 of         a protein encoded by a PRRSV ORF 5, in which one or more         (preferably 1-20, and more preferably 1-10) amino acid residues         may be conservatively substituted and which does not adversely         affect the antigenicity of the polypeptide,     -   f is an amino acid sequence selected from the group consisting         of those sequences listed under Hypervariable Region No. 3 in         the Table above, and     -   g is a carboxy group (a group of the formula —COOH), an amino         acid sequence corresponding to positions 129-200 of a protein         encoded by a PRSSV ORF 5 or a fragment thereof which does not         adversely affect the antigenicity of the polypeptide.

Accordingly, it is preferred that the present polynucleic acid, when used for immunoprotective purposes (e.g., in the preparation of a vaccine), contain at least one copy of ORF 5 from a high-replication isolate (i.e., an isolate which grows to a titer of 10⁶-10⁷ TCID₅₀ in, for example, CRL 11171 cells; also see the discussions in Experiments VIII-XI U.S. application Ser. No. 08/301,435).

On the other hand, the lv isolate VR 2431 appears to be a deletion mutant, relative to hv isolates (see Experiments III and VIII-XI U.S. application Ser. No. 08/301,435). The deletion appears to be in ORF 4, based on Northern blot analysis. Accordingly, when used for immunoprotective purposes, the present polynucleic acid preferably does not contain a region of ORF 4 from an hv isolate responsible for high virulence, and more preferably, excludes the region of ORF 4 which does not overlap with the adjacent ORF's 3 and 5.

It is also known (at least for PRRSV) that neither the nucleocapsid protein nor antibodies thereto confer immunological protection against PRRSV to pigs. Accordingly, the present polynucleic acid, when used for immunoprotective purposes, contains one or more copies of one or more regions from ORF's 2, 3, 4, 5 and 6 of a PRRSV isolate encoding an antigenic region of the viral envelope protein, but which does not result in the symptoms or histopathological changes associated with PRRS when administered to a pig. Preferably, this region is immunologically cross-reactive with antibodies to envelope proteins of other PRRSV isolates.

Similarly, the protein encoded by the present polynucleic acid confers protection against PRRS to a pig administered a composition comprising the protein, and antibodies to this protein are immunologically cross-reactive with the envelope proteins of other PRRSV isolates. More preferably, the present polynucleic acid encodes the entire envelope protein of a PRRSV isolate or a protein at least 80% homologous thereto and in which non-homologous residues are conservatively substituted, or alternatively a protein at least 98% homologous thereto. Most preferably, the present polynucleotide is one of the sequences shown in FIG. 1, encompassing at least one of the open reading frames recited therein.

Relatively short segments of polynucleic acid (about 20 bp or longer) in the genome of a virus can be used to screen or identify tissue and/or biological fluid samples from infected animals, and/or to identify related viruses, by methods described herein and known to those of ordinary skill in the fields of veterinary and viral diagnostics and veterinary medicine. Accordingly, a further aspect of the present invention encompasses an isolated (and if desired, purified) polynucleic acid consisting essentially of a fragment of from 15 to 2000 bp, preferably from 18 to 1000 bp, and more preferably from 21 to 100 bp in length, derived from ORF's 2-7 of a PRRSV genome (preferably the Iowa strain of PRRSV). Particularly preferably, the present isolated polynucleic acid fragments are obtained from a terminus of one or more of ORF's 2-7 of the genome of the Iowa strain of PRRSV, and most preferably, are selected from the group consisting of the primers described in Experiments 1 and 2 below and SEQ ID NOS:1-12, 22 and 28-34 of U.S. application Ser. No. 08/301,435.

The present invention also concerns a diagnostic kit for assaying a porcine reproductive and respiratory syndrome virus, comprising (a) a first primer comprising a polynucleotide having a sequence of from 10 to 50 nucleotides in length which hybridizes to a genomic polynucleic acid from an Iowa strain of porcine reproductive and respiratory syndrome virus at a temperature of from 25 to 75° C., (b) a second primer comprising a polynucleotide having a sequence of from 10 to 50 nucleotides in length, said sequence of said second primer being found in said genomic polynucleic acid from said Iowa strain of porcine reproductive and respiratory syndrome virus and being downstream from the sequence to which the first primer hybridizes, and (c) a reagent which enables detection of an amplified polynucleic acid. Preferably, the reagent is an intercalating dye, the fluorescent properties of which change upon intercalation into double-stranded DNA.

The present isolated polynucleic acid fragments can be obtained by: (i) digestion of the cDNA corresponding to (complementary to) the viral polynucleic acids with one or more appropriate restriction enzymes, (ii) amplification by PCR (using appropriate primers complimentary to the 5′ and 3′-terminal regions of the desired ORF(s) or to regions upstream of the 5′-terminus or downstream from the 3′-terminus) and cloning, or (iii) synthesis using a commercially available automated polynucleotide synthesizer.

Another embodiment of the present invention concerns one or more proteins or antigenic fragments thereof from a PRRS virus, preferably from the Iowa strain of PRRSV. As described above, an antigenic fragment of a protein from a PRRS virus (preferably from the Iowa strain of PRRSV) is at least 5 amino acids in length, particularly preferably at least 10 amino acids in length, and provides or stimulates an immunologically protective response in a pig administered a composition containing the antigenic fragment.

Methods of determining the antigenic portion of a protein are known to those of ordinary skill in the art (see the description above). In addition, one may also determine an essential antigenic fragment of a protein by first showing that the full-length protein is antigenic in a host animal (e.g., a pig). If the protein is still antigenic in the presence of an antibody which specifically binds to a particular region or sequence of the protein, then that region or sequence may be non-essential for immunoprotection. On the other hand, if the protein is no longer antigenic in the presence of an antibody which specifically binds to a particular region or sequence of the protein, then that region or sequence is considered to be essential for antigenicity.

Three hypervariable regions in ORF 5 of PRRSV have been identified by comparing the amino acid sequences of the ORF 5 product of all available PRRSV isolates (see, for example, FIG. 2D). Amino acid variations in these three regions are significant, and are not structurally conserved (FIG. 2D). All three hypervariable regions are hydrophilic and antigenic. Thus, these regions are likely to be exposed to the viral membrane and thus be under host immune selection pressure.

The present invention also concerns a protein or antigenic fragment thereof encoded by one or more of the polynucleic acids defined above, and preferably by one or more of the ORF's of a PRRSV, more preferably of the Iowa strain of PRRSV. The present proteins and antigenic fragments are useful in immunizing pigs against PRRSV, in serological tests for screening pigs for exposure to or infection by PRRSV (particularly the Iowa strain of PRRSV), etc.

For example, the present protein may be selected from the group consisting of the proteins encoded by ORF's 2-7 of VR 2385, ISU-22 (VR 2429), ISU-55 (VR 2430), ISU-1894, ISU-79 (VR 2474) and ISU-3927 (VR 2431) (e.g., one or more of the sequences shown in FIG. 2 and/or SEQ ID NOS:15, 17, 19, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 67, 69 and 71 of U.S. application Ser. No. 08/301,435); antigenic regions of at least one of these proteins having a length of from 5 amino acids to less than the full length of the protein; polypeptides having the minimum homology with the protein encoded by the PRSSV ORF indicated in Table 2 above; and polypeptides at least 97% homologous with a protein encoded by one of the ORF's 6-7 of VR 2385, VR 2429, VR 2430, ISU-1894, ISU-79 and VR 2431 (e.g., SEQ ID NOS:17, 19, 43, 45, 47, 49, 51, 53, 55, 57, 59 and 61 of U.S. application Ser. No. 08/301,435). Preferably, the present protein has a sequence encoded by an ORF selected from the group consisting of ORFs 2-5 of VR 2385, VR 2428, VR 2429, VR 2430, VR 2431, VR 2474 and ISU-1894 (see, for example, FIG. 2A-D); variants thereof which provide effective immunological protection to a pig administered the same and in which from 1 to 100 (preferably from 1 to 50 and more preferably from 1 to 25) deletions or conservative substitutions in the amino acid sequence exist; and antigenic fragments thereof at least 5 and preferably at least 10 amino acids in length which provide effective immunological protection to a pig administered the same.

More preferably, the present protein variant or protein fragment has a binding affinity (or association constant) of at least 1% and preferably at least 10% of the binding affinity of the corresponding full-length, naturally-occurring protein to a monoclonal antibody which specifically binds to the full-length, naturally-occurring protein (i.e., the protein encoded by a PRRSV ORF).

The present invention also concerns a method of producing a polypeptide, comprising expressing the present polynucleic acid in an operational expression system, and purifying the expressed polypeptide from the expression system. Suitable expression systems include those conventionally used for either in vitro or in vivo expression of proteins and polypeptides, such as a rabbit reticulocyte system for in vitro expression, and for in vivo expression, a modified or chimeric PRRSV (used to infect an infectable host cell line, such as MA-104, CRL 11171, PSP-36, PSP-36-SAH, MARC-145 and porcine alveolar macrophages), or a conventional expression vector containing the present polynucleic acid, under the operational control of a known promoter (e.g., a thymidine kinase promoter, SV40, etc.) for use in conventional expression systems (e.g., bacterial plasmids and corresponding host bacteria, yeast expression systems and corresponding host yeasts, etc.). The expressed polypeptide or protein is then purified or isolated from the expression system by conventional purification and/or isolation methods.

Other features of the invention will become apparent in the course of the following descriptions of exemplary embodiments, which are given for illustration of the invention, and are not intended to be limiting thereof.

EXAMPLE 1

Summary:

The sequences of ORFs 2 to 5 of one low virulence, one “moderate” virulence and one high virulence U.S. PRRSV isolate have been determined and analyzed. Comparisons with known sequences of other PRRSV isolates show that considerable sequence variations at both nucleotide and amino acid levels exist in ORFs 2 to 5 of seven U.S. isolates with differing virulence. However, ORFs 6 and 7 of these seven U.S. isolates are highly conserved (U.S. application Ser. No. 08/301,435). Extensive sequence variations were also found in ORFs 2 to 7 between the European LV and the U.S. isolates. The least virulent U.S. PRRSV isolate known (ISU-3927) displayed the most sequence variation, in comparison with other U.S. isolates.

The phylogenetic relationship of the U.S. isolates was also analyzed. Phylogenetic analysis of the ORFs 2 to 7 of the U.S. isolates indicated that there are at least three groups of PRRSV variants (or minor genotypes) within the major U.S. PRRSV genotype. Consequently, it is highly likely that a number of additional major or minor genotypes will be identified as more virus isolates from different geographic regions are examined.

Interestingly, the least virulent U.S. isolate known (ISU 3927) forms a branch distinct from other U.S. isolates. Analysis of the nucleotide and amino acid sequences also showed that the isolate ISU 3927 exhibits the most variations in ORFs 2 to 4, relative to other U.S. isolates. Many of these variations in isolate ISU 3927 result in non-conserved amino acid substitutions. However, these non-conserved changes in isolate ISU 3927, as compared to other U.S. isolates, do not appear to be limited to a particular region; they are present throughout ORFs 2 to 4. Therefore, a specific correlation between sequence variations and viral virulence is not yet fully elucidated (although certain positions in ORF 3 appear to be possibly related to virulence; see FIG. 2B, positions 30, 48, 54-56, 134, 140, 143, 147, 153, 206, and 215; amino acids at one or more of these positions may serve as a basis for mutating other known proteins encoded by a PRRSV ORF 3).

Results:

The amino acid sequence identity between seven U.S. PRRSV isolates was 91-99% in ORF 2, 86-98% in ORF 3, 92-99% in ORF 4 and 88-97% in ORF 5. The least virulent U.S. isolate known has higher sequence variations in the ORFs 2 to 4 than in ORFs 5 to 7, as compared to other U.S. isolates. Three hypervariable regions with antigenic potential were identified in the major envelope glycoprotein encoded by ORF 5.

Pairwise comparison of the sequences of ORFs 2 to 7 and phylogenetic tree analysis implied the existence of at least three groups of PRRSV variants (or minor genotypes) within the major genotype of U.S. PRRSV. The least virulent U.S. isolate known forms a distinct branch from other U.S. isolates with differing virulence. The results of this study have implications for the taxonomy of PRRSV and vaccine development.

FIG. 1 shows a nucleotide sequence comparison of ORFs 2 to 5 of U.S. isolates ISU 3927, ISU 22 and ISU 55 with other known PRRSV isolates. The nucleotide sequence of VR 2385 is shown on top, and only differences are indicated. The start codon of each ORF is indicated by +>, and the termination codon of each ORF is indicated by asterisks (*). The leader-mRNA junction sequences for subgenomic mRNAs 3, 4 and 3-1 are underlined, and the locations of the junction sequences relative to the start codon of each ORF are indicated by minus (−) numbers of nucleotides upstream of each ORF. The sequences of VR 2385 (U.S. application Ser. Nos. 08/131,625 and 08/301,435), VR 2332, ISU 79 and ISU 1894 (U.S. application Ser. No. 08/301,435) used in this alignment were previously reported.

Materials and Methods:

Cells and Viruses:

The ATCC CRL 11171 cell line was used to propagate the PRRSV. The cells were grown in Dulbecco's minimal essential medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1× antibiotics (penicillin G 10,000 unit/ml, streptomycin 10,000 mg/ml and amphotericin B 25 mg/ml).

Three U.S. isolates of PRRSV used in this study, designated as ISU 22, ISU 55 and ISU 3927, were isolated from pig lungs obtained from different farms in Iowa during PRRS outbreaks. All three isolates were plaque-purified three times on CRL 11171 cells before further experimentation. Comparative pathogenicity studies showed that isolate ISU 3927 is the least virulent isolate among 10 different U.S. PRRSV isolates. Isolate ISU 22 is a high virulence isolate and isolate ISU 55 is “moderately” pathogenic. All of the three virus isolates used in this experiment were at seventh passage.

Isolation of PRRSV Intracellular RNAs:

Confluent monolayers of CRL 11171 cells were infected with the three U.S. isolates of PRRSV, ISU 22, ISU 55 and ISU 3927, respectively, at a multiplicity of infection (m.o.i.) of 0.1. At 24 hrs. postinfection, the infected cells were washed three times with cold PBS buffer. The total intracellular RNAs were then isolated by guanidinium isothiocyanate and phenol-chloroform extraction (Stratagene). The presence of virus-specific RNA species in the RNA preparation was confirmed by Northern blot hybridization (data not shown). The total intracellular RNAs were quantified spectrophotometrically.

Reverse Transcription and Polymerase Chain Reaction (RT-PCR):

First strand complementary (c) DNA was synthesized from the total intracellular RNAs by reverse transcription using random primers as described previously (Meng et al., 1993, J. Vet. Diagn. Invest., 5:254-258). For amplification of the entire protein coding regions of the ORFs 2 to 5 of the three isolates of PRRSV, two sets of primers were designed on the basis of the sequences of VR 2385 and LV. Primers JM259 (5′-GGGGATCCTTTTGTGGAGCCGT-3′) and JM260 (5′-GGGGAATTCGGGATAGGGAATGTG-3′) amplified the sequence of ORFs 4 and 5, and primers XM992 (5′-GGGGGATCCTGTTGG-TAATAG(A)GTCTG-31 and XM993 (5′-GGTGAATTCGTTTTATTTCCCTCCGGGC-3′) amplified the sequence of ORFs 2 and 3. Unique restriction sites (EcoRI or BamHI) at the 5′ end of these primers were introduced to facilitate cloning. A degenerate base, G (A), was synthesized in primer XM 992 based on the sequences of VR 2385 and LV (Meulenberg et al., 1993; U.S. application Ser. No. 08/301,435). PCR was performed as described previously (Meng et al., 1993, J. Vet. Diagn. Invest., 5:254-258).

Cloning and Nucleotide Sequencing:

The RT-PCR products were analyzed by a 0.8% agarose gel electrophoresis. The two PCR fragments representing ORFs 2 and 3 as well as ORFs 4 and 5, respectively, were purified by the glassmilk procedure (GENECLEAN kit, BIO 101, Inc.). The purified fragments were each digested with BamHI and EcoRI, and cloned into the vector pSK+ as described previously (Meng et al., 1993). The E. Coli DH 5α cells were used for transformation of recombinant plasmids. White colonies were selected and grown in LB broth containing 100 mg/ml ampicillin. The E. Coli cells containing recombinant plasmid were lysed with lysozyme, and the plasmids were then isolated by using the Qiagen column (QIAGEN Inc.).

Plasmids containing viral inserts were sequenced with an automated DNA Sequencer (Applied Biosystem, Inc.). Three or more independent CDNA clones representing the entire sequence of ORFs 2 to 5 from each of the three PRRSV isolates were sequenced with universal and reverse primers. Several virus-specific primers, XM969 (5′-GATAGAGTCTGCCCTTAG-3′), XM970 (5′-GGTTTCACCTAGAATGGC-3′), XM1006 (5′-GCTTCTGAGATGAGTGA-3′), XM077 (5′-CAACCAGGCGTAAACACT-3′) and XM078 (5′-CTGAGCAATT ACAGAAG-3′), were also used to determine the sequence of ORFs 2 to 5.

Sequence Analyses:

Sequence data were combined and analyzed by using MacVector (International Biotechnologies, Inc.) and GeneWorks (IntelliGenetics, Inc.) computer software programs. Phylogenetic analyses were performed using the PAUP software package version 3.1.1 (David L. Swofford, Illinois Natural History Survey, Champaign, Ill.). PAUP employs the maximum parsimony algorithm to construct phylogenetic trees.

Results:

Nucleotide Sequence Analyses of ORFs 2 to 5:

The sequences of ORFs 2 to 5 of five PRRSV isolates, ISU 79, ISU 1894, ISU 22, ISU 55 and ISU 3927, were determined and compared with other known PRRSV isolates including VR 2385, VR 2332 and LV (Meulenberg et al., 1993). The sequences of ORFs 6 and 7 of isolates VR 2385, ISU 22, ISU 55, ISU 79, ISU 1894 and ISU 3927 were reported previously (U.S. application Ser. No. 08/301,435). The isolates used in this experiment have been shown to differ in pneumovirulence in experimentally-infected pigs (U.S. application Ser. Nos. 08/131,625 and 08/301,435). ISU 3927 is the least virulent isolate among ten different U.S. PRRSV isolates (U.S. application Ser. No. 08/131,625 and U.S. application Ser. No. 08/301,435).

Like other U.S. PRRSV isolates, ORFs 2 to 4 of these isolates overlapped each other (FIG. 1). However, unlike LV, ORFs 4 and 5 of the U.S. isolates are separated by 10 nucleotides (FIG. 1). ORFs 4 and 5 of LV overlapped by one nucleotide. The single nucleotide substitution from A of the start codon of ORF 5 in LV to T in the U.S. isolates places the start codon of ORF 5 of the U.S. isolates 10 nucleotides downstream of the ORF 4 stop codon. Therefore, a 10-nucleotide noncoding sequence appears between ORFs 4 and 5 of the known U.S. isolates (FIG. 1).

ORF 2 of ISU 79 is 3 nucleotides shorter than other U.S. isolates. The single nucleotide substitution from TGG to TAG just before the stop codon of ORF 2 creates a new stop codon in ISU 79 (FIG. 1). A 3-nucleotide deletion was also found in ORF 5 of ISU 3927, compared to other U.S. isolates (FIG. 1). The size of ORFs 2 to 5 of all the U.S. isolates are identical, except for the ORF 2 of ISU 79 and ORF 5 of ISU 3927, both of which are 3 nucleotides shorter than the other ORFs (FIG. 1).

Sequence comparisons of ORFs 2 to 5 of the seven U.S. PRRSV isolates shown in FIG. 1 indicate that there are considerable nucleotide sequence variations in ORFs 2 to 5 of the U.S. isolates (FIG. 1). The nucleotide sequence identity was 96-98% in ORF 2, 92-98% in ORF 3, 92-99% in ORF 4, and 90-98% in ORF 5 between VR 2385, VR 2332, ISU 22, ISU 55, ISU 79, and ISU 1894 (Table 3).

The least virulent isolate ISU 3927 has the most variations among the seven U.S. isolates (FIG. 1 and Table 3). The nucleotide sequence identity between ISU 3927 and other U.S. isolates was 93-94% in ORF 2, 89-90% in ORF 3, and 91-93% in ORF 4 (Table 3). Like ORFs 6 and 7 (U.S. application Ser. No. 08/301,435), ORF 5 of ISU 3927 has no significant changes except for a 3-nucleotide deletion (FIG. 1). ORF 5 of ISU 3927 shares 91-93% nucleotide sequence identity with the ORF 5 of other U.S. isolates (Table 3).

However, extensive sequence variation was found in ORFs 2 to 5 between LV and the U.S. isolates (FIG. 1 and Table 3). The nucleotide sequence identity between LV and the U.S. isolates was 65-67% in ORF 2, 61-64% in ORF 3, 63-66% in ORF 4, and 61-63% in ORF 5 (Table 3). Extensive genetic variations in ORFs 6 and 7 between LV and U.S. PRRSV also exists (U.S. application Ser. Nos. 08/131,625 and 08/301,435). These results indicate that the least virulent isolate ISU 3927 is also the most distantly related of the U.S. isolates, with genetic variations occurring mostly in ORFs 2 to 4.

The single nucleotide substitution from TGG to TAG before the stop codon in ORF 2 observed in ISU 79 was also present in isolates ISU 55 and ISU 3927, both of which produce seven sg mRNAs, but not in isolates ISU 22, ISU 1894 or VR 2385, which each synthesize only six sg mRNAs (U.S. application Ser. Nos. 08/131,625 and 08/301,435). The results indicate that the leader-mRNA 3-1 junction sequence of ISU 55 and ISU 3927 is very likely to be the same as ISU 79 (FIG. 1).

The leader-mRNA junction sequences for sg mRNAs 3 and 4 of ISU 79 and ISU 1894 were determined to be GUAACC at 89 nucleotides upstream of ORF 3 for sg mRNA 3, and UUCACC at 10 nucleotides upstream of ORF 4 for sg mRNA 4 (U.S. application Ser. No. 08/301,435; see also Experiment 2 below). A sequence comparison of isolates ISU 22, ISU 55 and ISU 3927 with isolates VR 2385, ISU 79 and ISU 1894 indicates that the leader-mRNA junction sequences for sg mRNAs 3 and 4 are conserved among the U.S. isolates (FIG. 1).

Analysis of the Deduced Amino Acid Sequences Encoded by ORFs 2 to 5:

FIG. 2 shows the alignment of the deduced amino acid sequences of ORF 2 (A), ORF 3 (B), ORF 4 (C) and ORF 5 (D) of U.S. isolates ISU 22, ISU 55 and ISU 3927 with other known PRRSV isolates. The sequence of VR 2385 is shown on top, and only differences are indicated. Deletions are indicated by

-   (−). The proposed signal peptide sequence in the ORF 5 of LV (D) is     underlined (Meulenberg et al., 1995). Three hypervariable regions     with antigenic potentials in ORF 5 (D) were indicated by asterisks     (*). The published sequences used in this alignment were LV     (Meulenberg et al., 1993), VR 2385 (U.S. application Ser. Nos.     08/131,625 and 08/301,435), VR 2332, ISU 79 and ISU 1894 (U.S.     application Ser. No. 08/301,435).

On the basis of its high content of basic amino acids and its hydrophilic nature, the translation product of ORF 7 is predicted to be the nucleocapsid protein (U.S. application Ser. Nos. 08/131,625 and 08/301,435; Meulenberg et al., 1993; Conzelmann et al., 1993; Mardassi et al., 1994). The ORF 6 product lacks a potential amino-terminal signal sequence and contains several hydrophobic regions which may represent the potential transmembrane fragments. Therefore, the ORF 6 product was predicted to be the M protein (U.S. application Ser. Nos. 08/131,625 and 08/301,435; Meulenberg et al., 1993; Conzelmann et al., 1993).

Computer analysis shows that the products encoded by ORFs 2 to 5 of the U.S. isolates all have hydropathy characteristics reminiscent of membrane-associated proteins. The translation products of ORFs 2 to 5 each contain a hydrophobic amino terminus. The N-terminal hydrophobic sequences may function as a signal sequence for each of these ORFs, and they may be involved in the transportation of ORFs 2 to 5 to the endoplasmic reticulum of infected cells. At least one additional hydrophobic domain in each of ORFs 2 to 5 was found at the carboxy termini. These additional hydrophobic domains may function as membrane anchors.

The deduced amino acid sequences of ORFs 2 to 5 of the seven U.S. isolates examined also varied considerably (FIG. 2), indicating that most of the nucleotide differences observed in FIG. 1 are not silent mutations. The amino acid sequence identity between VR 2385, VR 2332, ISU 22, ISU 55, ISU 79, and ISU 1894 was 95-99% in ORF 2, 90-98% in ORF 3, 94-98% in ORF 4, and 88-97% in ORF 5 (Table 3).

Again, the least virulent isolate ISU 3927 displayed more variations with other U.S. isolates in ORFs 2 to 4 (FIG. 2 and Table 3) than in ORFs 5 to 7 (U.S. application Ser. No. 08/301,435 and Table 3). ORFs 2 to 5 of LV share only 57-61%, 55-56%, 65-67%, and 51-55% amino acid sequence identity with those ORFs of the U.S. isolates, respectively (Table 3). Deletions or insertions were found throughout ORFs 2 to 5 in comparing European LV and U.S. isolates (FIG. 2).

Sequence comparison of the ORF 5 product showed that the N-terminal region of ORF 5 is extremely variable, both (a) between U.S. isolates and LV and also (b) among the various U.S. isolates (FIG. 2D). In LV, the first 32-33 amino acid residues of ORF 5 may represent the signal sequence (Meulenberg et al., 1995; FIG. 2D). Therefore, the potential signal sequence of ORF 5 in all the PRRSV isolates is very heterogeneous. This heterogeneity is not due to any host immune selection pressure, because the signal peptide will be cleaved out and not be present in mature virions.

Three additional hypervariable regions were also identified by comparing the amino acid sequences of ORF 5 of all the PRRSV isolates available (FIG. 2D). Amino acid variations in these three regions are significant, and are not structurally conserved (FIG. 2D). Computer analysis indicates that all three hypervariable regions are hydrophilic and antigenic. Thus, it is likely that these regions are exposed to the viral membrane and are under host immune selection pressure. However, further experiments may be necessary to confirm the specific functions of these hypervariable regions as antigenic determinants in the ORF 5 envelope protein.

The Phylogenetic Relationships Among U.S. Isolates of PRRSV:

It has been shown previously that U.S. PRRSV and European PRRSV represent two distinct genotypes, based on analysis of the M and N genes (U.S. application Ser. No. 08/301,435). To determine the phylogenetic relationships of U.S. PRRSV isolates, ORFs 2 to 7 of the seven U.S. PRRSV isolates shown in FIGS. 1 and 2 were first aligned with the GeneWorks program (intelligenetics, Inc.). The PAUP program (David L. Swofford, Illinois Natural History Survey, Champaign, Ill.) was then used to construct phylogenetic tree illustrating relationship among U.S. isolates of PRRSV.

The phylogenetic tree of FIG. 3 was constructed by maximum parsimony methods with the aid of the PAUP software package version 3.1.1. The branch with the shortest length (most parsimonious) was found by implementing the exhaustive search option. The branch lengths (numbers of amino acid substitutions) are given above each branch. The sequences used in the analysis are LV, VR 2385, VR 2332, ISU 79 and ISU 1894.

The phylogenetic tree indicates that at least three groups of variants (or minor genotypes) exist within the major U.S. PRRSV genotype. The least virulent U.S. PRRSV isolate ISU 3927 forms a branch distinct from other U.S. isolates (FIG. 3). Isolates ISU 22, ISU 79, ISU 1894, and VR 2332 form another branch, representing a second minor genotype. The third minor genotype is represented by isolates ISU 79 and VR 2385 (FIG. 3). A very similar tree was also obtained by analyzing the last 60 nucleotides of ORF 1b of the seven U.S. isolates presented in FIG. 1 (data not shown). Identical tree topology was also produced by the unweighted pair-group method with arithmetic mean (UPGMA) using the GeneWorks program (data not shown).

In summary, the different genotypes of PRRSV have been confirmed and further elucidated. At least three minor genotypes within the major genotype of U.S. PRRSV have been identified, based on an analysis of the sequence of ORFs-2 to 7. Genetic variations not only between the European PRRSV and the U.S. PRRSV but among the U.S. PRRSV isolates have also been further confirmed as well, indicating the heterogeneous nature of PRRSV. The least virulent U.S. PRRSV isolate ISU 3927 has unexpectedly high sequence variations in ORFs 2 to 4, as compared to other U.S. isolates. TABLE 3 Nucleotide and deduced amino acid sequence identities (%) of ORFs 2 to 5 of PRRSV ORF 2 VR2385 ISU22 ISU55 ISU79 ISU1894 ISU3927 VR2332 LV VR2385 ** 97 96 96 95 91 98 58 ISU22 97 ** 96 98 96 93 99 59 ISU55 98 97 ** 96 95 91 97 61 ISU79 96 97 97 ** 96 91 98 60 ISU1894 96 97 96 96 ** 93 96 57 ISU3927 94 94 94 93 93 ** 93 58 VR2332 97 98 97 98 97 94 ** 59 LV 65 66 66 67 66 65 66 ** ORF 3 VR2385 ** 91 94 92 90 87 91 55 ISU22 92 ** 93 96 96 88 98 56 ISU55 94 93 ** 94 93 87 94 56 ISU79 94 96 94 ** 95 87 96 56 ISU1894 92 97 93 96 ** 86 96 55 ISU3927 90 90 89 90 90 ** 87 55 VR2332 93 98 94 97 97 90 ** 56 LV 64 63 62 63 63 61 63 ** ORF 4 VR2385 ** 94 96 94 95 83 94 66 ISU22 93 ** 94 97 99 93 98 66 ISU55 96 94 ** 96 96 93 95 67 ISU79 93 97 94 ** 98 92 96 66 ISU1894 92 98 94 96 ** 93 98 66 ISU3927 91 93 92 91 91 ** 92 67 VR2332 94 99 95 97 98 92 ** 65 LV 66 66 63 65 66 65 65 ** ORF 5 VR2385 ** 90 91 88 89 91 89 54 ISU22 93 ** 90 94 96 92 97 52 ISU55 94 92 ** 89 89 90 89 51 ISU79 91 95 91 ** 95 89 94 53 ISU1894 92 97 90 94 ** 91 96 53 ISU3927 91 93 91 91 91 ** 91 55 VR2332 93 98 91 95 97 92 ** 53 LV 63 63 63 61 62 63 63 ** Note: The amino acid sequence comparisons are presented in the upper right half, and the nucleotide sequence comparisons are presented in the lower left half.

EXAMPLE 2

During the replication of PRRSV, six subgenomic mRNAs (sg mRNAs), in addition to the genomic RNA, are synthesized. These sg mRNAs were characterized in this experiment.

The sg mRNAs of PRRSV form a 3′-coterminal nested set in PRRSV-infected cells. Each of these sg mRNAs is polycistronic and contains multiple open reading frames, except for sg mRNA 7 (as shown by Northern blot analysis using ORF-specific probes). The sg mRNAs were not packaged into virions, and only the genomic RNA was detected in purified virions, suggesting that the encapsidation signal of PRRSV is likely localized in the ORF 1 region.

The numbers of sg mRNAs in PRRSV-infected cells varies among PRRSV isolates with differing virulence. An additional species of sg mRNA in some PRRSV isolates was shown in Experiment 1 above to be derived from the sequence upstream of ORF 4, and has been designated as sg mRNA 3-1.

The leader-mRNA junction sequences of sg mRNAs 3 and 4 of isolates ISU 79 and ISU 1894, as well as sg mRNA 3-1 of the isolate ISU 79, contain a common six nucleotide sequence motif, T(G)TA(G/C)ACC. Sequence analysis of the genomic RNA of these two U.S. isolates and comparison with Lelystad virus (LV) revealed heterogeneity of the leader-mRNA junction sequences among PRRSV isolates. The numbers, locations and the sequences of the leader-mRNA junction regions varied between U.S. isolates and LV, as well as among U.S. isolates. The last three nucleotides, ACC, of the leader-mRNA junction sequences are invariable. Variations were found in the first three nucleotides.

By comparing the 5′-terminal sequence of sg mRNA 3-1 with the genomic sequence of ISU 79 and ISU 1894, it was found that a single nucleotide substitution, from T in ISU 1894 to C in ISU 79, led to a new leader-mRNA junction sequence in ISU 79, and therefore, an additional species of sg mRNA (sg mRNA 3-1). A small ORF, designated as ORF 3-1, with a coding capacity of 45 amino acids was identified at the 5′-end of sg mRNA 3-1.

Materials and Methods

Viruses and cells. The PRRSV isolates used (ISU 22, ISU 55, ISU 79, ISU 1894 and ISU 3927) were isolated from pig lungs obtained from different farms in Iowa. A continuous cell line, ATCC CRL 11171, was used for isolation and growth (culturing) of viruses. These PRRSV isolates were biologically cloned by three rounds of plaque purification and grown on the CRL 11171 cells. All of the virus isolates used in this study were at the seventh passage.

ISU 22 and ISU 79 are highly pathogenic and produce from 50 to 80% consolidation of the lung tissues in experimentally-infected five-week-old caesarean-derived colostrum-deprived pigs necropsied at 10 days post-inoculation. By contrast, ISU 55, ISU 1894 and ISU 3927 are of low pathogenicity and produce only 10 to 25% consolidation of lung tissues in the same experiment (U.S. application Ser. Nos. 08/131,625 and 08/301,435).

Preparation of virus-specific total intracellular RNAs, poly (A)⁺ RNA and virion RNA. Confluent monolayers of CRL 11171 cells were infected with different isolates of PRRSV at the seventh passage at a multiplicity of infection (m.o.i.) of 0.1. PRRSV-specific total intracellular RNAs were isolated from PRRSV-infected cells by a conventional guanidinium isothiocyanate method (Stratagene). The poly (A)⁺ RNA was enriched from the total intracellular RNAs by oligo (dT)-cellulose column chromatography (Invitrogen).

For isolation of PRRSV virion RNA, confluent CRL 11171 cells were infected with isolate ISU 3927 of PRRSV at a m.o.i. of 0.1. When more than 70% of the infected cells showed a cytopathic effect, the cultures were frozen and thawed three times, and the culture medium was clarified at 1200×g for 20 min. at 4° C. The virus was then precipitated with polyethylene glycol and subsequently purified by cesium chloride gradient centrifugation as described in U.S. application Ser. No. 08/131,625. The purified virus was treated with RNase A at a final concentration of 20 μ/ml for 90 min. at 37° C. The virus was then pelleted, and the virion RNA was isolated using a conventional guanidinium isothiocyanate method.

cDNA synthesis and polymerase chain reaction. cDNA was synthesized from total intracellular RNAs by reverse transcription using random primers and amplified by the polymerase chain reaction (RT-PCR) as described previously (Meng et al., 1993, J. Vet. Diagn. Invest., 5:254-258).

Northern blot analyses. Ten μg of total intracellular RNAs from virus infected cells and mock-infected cells were used per lane in a formaldehyde-agarose gel. For separation of poly (A)⁺ RNA and virion RNA, fifteen ng of virion RNA and 0.2 μg of poly (A)⁺ RNA were loaded per lane. The RNA was denatured with formaldehyde according to a conventional method (Sambrook et al, “Molecular Cloning: A Laboratory Manual”, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.). Electrophoretic separation of RNA, RNA blotting, and hybridization were performed as described in U.S. application Ser. No. 08/131,625. In some experiments, glyoxal-DMSO agarose gels were also performed as described in U.S. application Ser. No. 08/131,625.

For preparation of probes, a specific cDNA fragment from each of the ORFs lb to 7 was generated by RT-PCR with ORF-specific primers. The primers were designed in such a way that each primer pair amplifies only a specific fragment of a given ORF, and the overlapping, neighboring ORFs are not included in any given cDNA probe. The primer pairs for generating cDNA probes representing ORFs lb through 7 are IM729/IM782 for ORF 1b, IM312/IM313 for ORF 2, XM1022/IM258 for ORF 3, XM1024/XMI 023 for ORF 4, PP287/PP286 for ORF 5, PP289/XM780 for ORF 6, and PP285/PP284 for ORF 7 (Table 4).

Cloning, sequencing and nucleotide sequence analyses. Primers for RT-PCR were designed on the basis of PRRSV isolate VR 2385 sequences, which amplified the entire protein coding regions of ORFs 2 to 5 of PRRSV isolates ISU 79 and ISU 1894. Primers JM259 and JM260 were used for amplification of ORFs 4 and 5, and XM992 and XM993 for amplification of ORFs 2 and 3 (Table 4). Unique restriction sites (EcoRI and BamHI) at the termini of the PCR products were introduced, thus enabling a cassette approach to replacement of these ORFs.

The PCR products of ORFs 2-3 and ORFs 4-5 of ISU 79 and ISU 1984 were each digested with EcoRI and BamHI, then purified and cloned into vector pSK+ as described previously (Meng et al., 1993, J. Vet. Diagn. Invest., 5:254-258). Plasmids containing viral inserts were sequenced with a conventional automated DNA sequencer (Applied Biosystem, Inc.). At least three cDNA clones representing the entire sequence of ORFs 2 to 5 from each virus isolate were sequenced with universal and reverse primers, as well as other virus-specific sequencing primers (XM969, XM970, XM1006, XM078 and XM077; see Table 4).

To determine the leader-mRNA junction sequences of sg mRNAs 3, 4 and 3-1, primer pair IM755 and DP586 (Table 4) was used for RT-PCR to amplify the corresponding 5′-terminal sequences. The resulting PCR products were purified and sequenced by direct PCR sequencing using virus specific primers XMD77 and XM141 (Table 4). The sequences were combined and analyzed by MacVector (International Biotechnologies, Inc.) and GeneWorks (IntelliGenetics, Inc) computer software programs.

Oligonucleotides. The synthetic oligonucleotides used in this study were summarized in Table 4. These oligonucleotides were synthesized as single stranded DNA using an automated DNA synthesizer (Applied Biosystem) and purified by high pressure liquid chromatography (HPLC).

Results

Sg mRNAs are not packaged into PRRSV virions. To determine whether the sg mRNAs of PRRSV are packaged, virions of PRRSV isolate ISU 3927 were purified by CsCl gradient. The purified virions were treated with RNase A before pelleting the virion and extracting RNA, to remove any RNA species which may have adhered to the virion surface. RNAs from RNase A-treated virions along with the total intracellular RNAs from isolate ISU 3927 of PRRSV-infected cells were separated in a formaldehyde gel and hybridized with a probe generated from the 3′-terminal sequence of the viral genome by PCR with primers PP284 and PP285 (U.S. application Ser. No. 08/131,625; Table 4).

Only the genomic RNA was detected in the purified virions of PRRSV isolate ISU 3927 (FIG. 4), and no detectable amounts of sg mRNAs were observed in the purified virions even after 3 weeks exposure. In contrast, seven species of sg mRNAs, in addition to the genomic RNA, were detected in ISU 3927-infected cells (FIG. 4). Similar results were observed with two other U.S. isolates, ISU 55 and ISU 79.

Variation in the numbers of the sg mRNAs among U.S. PRRSV isolates with differing virulence. All arteriviruses known prior to the present invention, including U.S. PRRSV and European PRRSV, have been shown to produce six sg mRNAs, except for three LDV variants (LDV-P, LDV-a and LDV-v), which synthesize seven sg mRNAs. However, a nested set of six sg mRNAs is produced in the LDV-C strain.

To compare if there are any variations in the sg mRNAs among U.S. PRRSV isolates, confluent monolayers of CRL 11171 cells were infected with five different isolates of U.S. PRRSV with differing virulence at a m.o.i. of 0.1. Total intracellular RNAs were isolated from virus-infected cells at 24 h post-infection. A cDNA fragment was generated from the extreme 3′-end of the viral genome by PCR with primers PP284 and PP285 (Table 4). The cDNA fragment was labeled with ³²P-dCTP by the random primer extension method, and hybridized with the total intracellular RNAs (separated on a formaldehyde gel).

Analyses of the RNAs showed that a nested set of six or more sg mRNAs, in addition to the genomic RNA, was present in cells infected with one of the five isolates of U.S. PRRSV with differing virulence (FIG. 5). Similar results were obtained when the total intracellular RNAs were separated on a glyoxal-DMSO agarose gel. PRRSV isolates ISU 55, ISU 79 and ISU 3927 produced seven easily distinguishable sg mRNAs, whereas isolates ISU 22 and ISU 1894 produced six sg mRNAs (FIG. 5). The U.S. PRRSV isolate VR 2385 also produces six sg mRNAs (U.S. application Ser. No. 08/131,625). An additional species of sg mRNA was located between sg mRNAs 3 and 4, and was designated as sg mRNA 3-1. The sg mRNAs differed little, if any, in size among the five isolates of PRRSV (FIG. 5). There appears to be no correlation, however, between the pneumovirulence and the numbers of the sg mRNAs observed in these five isolates.

Sg mRNA 3-1 is not a defective-interfering RNA and is not a result of nonspecific binding of the probes to ribosomal RNAs. It has been shown that, in coronaviruses, a variety of defective interfering RNA (DI RNA) of different sizes were generated when MHV was serially passaged in tissue culture at a high m.o.i. DI RNAs were also observed in cells infected with torovirus during undiluted passage. Therefore, the possibility of sg mRNA 3-1 of PRRSV being a DI RNA was investigated.

To exclude this possibility, the original virus stock of PRRSV isolate ISU 79, which produces the additional species of sg mRNA 3-1, was passaged four times in CRL 11171 cells at different m.o.i. of 0.1, 0.01 and 0.001, respectively. In a control experiment, four undiluted passages of the original virus stock of ISU 79 were performed. After four passages, total intracellular RNAs were isolated from virus-infected cells and Northern blot analysis was repeated with the same probe generated from the extreme 3′-end of the viral genome.

Analyses of the sg mRNAs showed that the additional species of sg mRNA 3-1 was still present in all RNA preparations with different m.o.i., as well as in RNA preparations from undiluted passages (FIG. 6A). Moreover, there was no interference or reduction in the synthesis of other sg mRNAs in the presence of sg mRNA 3-1, as is usually the case with DI RNA.

It has been demonstrated that the DI RNAs of MHV disappeared after two high-dilution passages. Therefore, if the original virus stock of ISU 79 contained DI RNA, then the DI RNA should disappear after four high-dilution passages. The experimental data above suggests that, unlike DI RNA, the replication of sg mRNA 3-1 is independent of the amount of standard virus. Thus, sg mRNA 3-1 is not a DI RNA.

In Northern blot analysis of total intracellular RNAS, the probes may nonspecifically bind to the 18S and 28S ribosomal RNAs, which are abundant in total cytoplasmic RNA preparations. Alternatively, the abundant ribosomal RNAs may cause retardation of virus-specific sg mRNAs which may co-migrate corrugate with the ribosomal RNAs in the gel.

Two additional bands due to the nonspecific binding of probes to the ribosomal RNAs have been observed in LV-infected cells and LDV-infected cells. Therefore, it is possible that sg mRNA 3-1 of PRRSV is due to the nonspecific binding of probes to the ribosomal RNAs.

To rule out this possibility, polyadenylated RNA was isolated from total intracellular RNAs of CRL 11171 cells infected with either of two PRRSV isolates, ISU 55 and ISU 79. Both ISU 55 and ISU 79 produce the additional species of sg mRNA 3-1 (FIG. 5). Northern blot analysis of the polyadenylated RNA showed that the additional species of sg mRNA 3-1 in cells infected with either of these two isolates was still present (FIG. 6B), indicating that sg mRNA 3-1 is not due to the nonspecific binding of a probe to the ribosomal RNAS.

The sg mRNAs represent a 3′-coterminal nested set and the sg mRNA 3-1 is derived from the sequence upstream of ORF 4. Six sg mRNAs, in addition to the genomic RNA, are detected in cells infected with VR 2385 using a cDNA probe from the extreme 3′-end of the viral genome (U.S. application Ser. No. 08/131,625). Thus, like Berne virus (BEV), LDV, EAV, coronaviruses and LV, the replication of U.S. PRRSV also requires the synthesis of a 3′-coterminal nested set of sg mRNAs (U.S. application Ser. Nos. 08/131,625 and 08/301,435).

To analyze these sg mRNAs in more detail, seven cDNA fragments specific for each of ORFs lb through 7 were amplified by PCR. The design of primers for PCR was based on the sequence of VR 2385. The sequences and locations of the primers, IM729 and IM782 for ORF 1b, IM312 and IM313 for ORF 2, XM1022 and IM258 for ORF 3, XM1024 and XM1023 for ORF 4, PP286 and PP287 for ORF 5, PP289 and XM780 for ORF 6, and PP284 and PP285 for ORF 7 and the 3′ noncoding region (NCR), are shown in Table 4. The primers were designed in such a way that each set of primers will only amplify a fragment from a particular ORF, and the overlapping sequences between neighboring ORFs are not included in any given fragment. Therefore, each of these seven DNA fragments represents only one particular ORF except for fragment 7, which represents both ORF 7 and the 3′-NCR.

These seven DNA fragments were labeled with ³²P-dCTP and hybridized to Northern blots of total intracellular RNAs extracted from cells infected with either of two U.S. isolates of PRRSV, ISU 1894 and ISU 79. Total intracellular RNAs isolated from mock-infected CRL 11171 cells were included as a control.

Northern blot analyses showed that Probe 1, generated from ORF 1b, hybridized only with the genomic RNA. Probes 2 through 7 each hybridized with one more additional RNA species besides the genomic RNA (FIG. 7). The results indicate that a 3′-coterminal nested set of six (ISU 1894) or more (ISU 79) sg mRNAs is formed in PRRSV-infected cells (FIGS. 7A and 7B), with the smallest 3′-terminal RNA (sg mRNA 7) encoding ORF 7. The sg mRNAs of U.S. PRRSV all contain the 3′-end of the genomic RNA, but extend for various distances towards the 5′-end of the genome, depending on the size of the given sg mRNA.

The sg mRNA 3-1 of PRRSV isolate ISU 79 hybridized with probes 4 through. 7, but not with probes 1, 2 and 3 (FIG. 7B), suggesting that sg mRNA 3-1 contains ORFs 4 through 7 as well as the 3′-NCR. Therefore, sg mRNA 3-1 is generated from the sequence upstream of ORF 4.

A single nucleotide substitution leads to the acquisition of the additional species of sg mRNA 3-1. Northern blot hybridization data showed that sg mRNA 3-1 is derived from the sequence upstream of ORF 4 (FIG. 7B). To determine the exact location and the leader-mRNA junction sequence of sg mRNA 3-1, a set of primers, IM755 and DP586, was designed (Table 4). The forward primer IM755 was based on the 3′-end of the leader sequence of VR 2385, and the reverse primer DP586 is located in ORF 4 (Table 4).

RT-PCR with primers IM755 and DP586 was performed using total intracellular RNAs isolated from cells infected with either of ISU 1894 or ISU 79. ISU 79 produces sg mRNA 3-1, but ISU 1894 does not (FIG. 5). A 30-second PCR extension time was applied to preferentially amplify the short fragments representing the 5′-terminal sequences of sg mRNAs 3, 4 and 3-1.

Analysis of the RT-PCR products showed that two fragments with sizes of about 1.1 kb and 0.45 kb were amplified from the total RNAs of ISU 1894 virus-infected cells (FIG. 8A). These two fragments represent 5′-portions of sg mRNAs 3 and 4, respectively. In addition to the two fragments observed in the isolate of ISU 1894, a third fragment of about 0.6 kb representing the 5′-portion of sg mRNA 3-1 was also amplified from total RNAs of cells infected with ISU 79 (FIG. 8A).

To determine the leader-mRNA junction sequences of sg mRNAs 3, 4 and 3-1, the RT-PCR products of ISU 79 and ISU 1894 were purified from an agarose gel using a GENECLEAN kit (Bio 101, Inc.), and sequenced directly with an automated DNA Sequencer (Applied Biosystems). The primers used for sequencing the 5′-end of the RT-PCR products (XM141 and XM077, Table 4) were designed on the basis of the genomic sequences of ISU 79 and ISU 1894 (FIG. 9). The leader-mRNA junction sequences (in which the leader joins the mRNA body during the synthesis of sg mRNAs) of sg mRNAs 3, 4, and 3-1 of the two U.S. PRRSV isolates were determined by comparing the sequences of the 5′-end of the sg mRNAs and the genomic RNA of the two isolates (FIG. 8B).

The leader-mRNA junction sequences of sg mRNAs 3 and 4 of ISU 1894 and ISU 79 were identical. For sg mRNA 3, the leader-junction sequence (GUAACC) is located 89 nucleotides upstream of ORF 3. For sg mRNA 4, UUCACC is located 10 nucleotides upstream of ORF 4 (FIG. 8B and FIG. 9). The leader-mRNA junction sequence of sg mRNA 3-1 of ISU 79 is UUGACC, located 236 nucleotides upstream of ORF 4 (FIGS. 8B and 9).

Sequence alignment of the genomic sequences of ISU 79 and ISU 1894 shows that a single nucleotide substitution, from T in ISU 1894 to C in ISU 79, leads to the acquisition of an additional leader-mRNA junction sequence, UUGACC, in ISU 79 (FIGS. 8B and 9). Therefore, an additional species of sg mRNA (3-1) is formed (FIG. 5). In addition to ORFs 4 to 7 contained within sg mRNA 4, sg mRNA 3-1 contains at the 5′-end an additional small ORF (ORF 3-1) with a coding capacity of 45 amino acids (FIG. 9). This small ORF stops just one nucleotide before the start codon of ORF 4.

Sequence analyses of ORFs 2 to 7 of two U.S. isolates reveal heterogeneity of the leader mRNA junction sequences. ORFs 2 to 5 of ISU 79 and ISU 1894 were cloned and sequenced (see Experiment 1 above). ISU 79 produces seven easily distinguishable sg mRNAs, whereas ISU 1894 produces six distinguishable sg mRNAs (FIGS. 5 and 7). At least three cDNA clones at any given region of ORFs 2 to 5 were sequenced for each virus isolate, using universal and reverse primers as well as virus-specific primers XM969, XM970, XM1006, XM078, and XM077 (Table 4). The sequences of ORFs 6 and 7 of ISU 1894 and ISU 79 are disclosed in U.S. application Ser. No. 08/301,435.

Sequence analysis showed that the ORFs 2 to 7 of ISU 79 and ISU 1894 overlap each other except for a 10-nucleotide noncoding region between ORF 4 and ORF 5. The same observation was previously made for VR 2385 (U.S. application Ser. No. 08/301,435). This is very unusual, since all members of the proposed Arteriviridae family, including LV, contain overlapping ORFs. However, the ORFs of coronaviruses are separated by intergenic noncoding sequences. Therefore, U.S. PRRSV appears to be somewhat similar to the coronaviruses in terms of the genomic organization in junction regions of ORFs 4 and 5.

ORF 2 of ISU 1894 was one amino acid longer than that of ISU 79 (FIG. 9). The stop codon of ORF 2, TAG, was changed to TGG in ISU 1894 immediately followed by a new stop codon (TGA) in ISU 1894 (FIG. 9). The sizes of other ORFs of ISU 79 and ISU 1894 were identical (FIG. 9). There were no deletions or insertions in ORFs 2 to 7 of these isolates. However, numerous substitutions are present throughout the entire sequence of ORFs 2 to 7 between ISU 79 and ISU 1894 (FIG. 9).

The numbers and locations of the determined or predicted leader-mRNA junction sequences varied between ISU 1894 and ISU 79 (FIG. 9). In addition to the regular leader-mRNA 4 junction sequence, TTCACC, 10 nucleotides upstream of ORF 4, there was an additional leader-mRNA 3-1 junction sequence (TTGACC) located 236 nucleotides upstream of ORF 4 in ISU 79 (FIG. 9). The leader-mRNA junction sequences of sg mRNAs 4 and 3-1 were separated by 226 nucleotides, which correlated with the estimated sizes of sg mRNAs 4 and 3-1 observed in Northern blot analysis (FIG. 5) and RT-PCR amplification (FIG. 8A).

The leader-mRNA 3 junction sequence is identical between ISU 1894 and ISU 79, GTAACC, located 89 nucleotides upstream of ORF 3. The predicted leader-mRNA junction sequences of sg mRNAs 2 and 6 of ISU 1894 and ISU 79 were also the same (FIG. 9).

However, the predicted leader-mRNA 5 junction sequences of ISU 1894 and ISU 79 are different (FIG. 9). There are 3 potential leader-mRNA 5 junction sequences for ISU 79 (GCAACC, GAGACC and TCGACC, located 55, 70 and 105 nucleotides upstream of ORF 5, respectively). Two potential leader-mRNA 5 junction sequences were also found in ISU 1894 (GAAACC and TCGACC, located 70 and 105 nucleotides upstream of ORF 5, respectively) (FIG. 9). The differences were due to the two-nucleotide substitutions in the predicted leader-mRNA 5 junction sequences of these isolates (FIG. 9).

In addition to the leader-mRNA 7 junction sequence 15 nucleotides upstream of ORF 7, an additional leader-mRNA 7 junction sequence was found (ATAACC), located 129 nucleotides upstream of ORF 7 in each of these two isolates (FIG. 9). However, the sg mRNA corresponding to this additional leader-mRNA 7 junction sequence was not clearly distinguishable from the abundant sg mRNA 7 which produced a widely-diffused band-in the Northern blot (FIGS. 5, 6 and 7).

Variations in the numbers and locations of the leader-mRNA junction sequences between LV and the two U.S. isolates analyzed in this experiment were also found by comparing the leader-mRNA junction sequences of LV with those of the two U.S. isolates ISU 1894 and ISU 79. Taken together, these data indicate that the sg mRNAs of PRRSV are polymorphic, and the numbers and the exact sizes of the sg mRNAs depend on the particular PRRSV isolate analyzed. However, a nested set of six sg mRNAs most likely reflects the standard arterivirus genome organization and transcription. TABLE 4 Synthetic oligonucleotides used in Experiment 2 OLigo Name Sequence Location (nucteotides)^(a) Polarity^(b) IM729 5′-GACTGATGGTCTGGAAAG-3′ ORF1b, −507 to −490 upstream of ORF2 + IM782 5′-CTGTATCCGATTCAAACC-3′ ORF1b, −180 to −163 upstream of ORF2 − IM312 5 -AGGTTGGCTGGTGGTCTT-3′ ORF2, 131 to 148 downstream of ORF2 + IM313 5′-TCGCTCACTACCTGTTTC-3′ ORF2, 381 to 398 downstream of ORF2 − XM1022 5′-TGTGCCCGCCTTGCCTCA-3′ ORF3, 168 to 175 downstream of OEF3 + IM268 5′-AAACCAATTGCCCCCGTC-3′ ORF3, 520 to 537 downstream of ORF3 − XM1024 5′-TATATCACTGTCACAGCC-3′ ORF4, 232 to 249 downstream of ORF4 + XM1023 5′-CAAATTGCCAACAGAATG-3′ ORF4, 519 to 536 downstream of ORF4 − PP287 5′-CAACTTGACGCTATGTGAGC-3′ ORF5, 129 to 148 downstream of ORF5 + PP286 5′-GCCGCGGAACCATCAAGCAC-3′ ORF5, 538 to 667 downstream of ORF5 − PP289 5′-GACTGCTAGGGCTTCTGCAC-3′ ORF6, 119 to 138 downstream of ORF6 + XM780 5′-CGTTGACCGTAGTGGAGC-3′ ORF6, 416 to 433 downstream of ORF6 − PP285 5′-CCCCATTTCCCTCTAGCGACTG-3′ ORF7, 157 to 178 downstream of ORF7 + PP284 5′-CGGCCGTGTGGTTCTCGCCAAT-3′ 3′NCR, −27 to −6 upstream of poly (A) − JM260 5′-GGGGAATTCGGGATAGGGAATGTG-3′ ORF3, 338 to 356 downstream of ORF3 + JM259 5′-GGGGATCCTTTTGTGGAGCCGT-3′ ORF6, 34 to 52 downstream of ORF6 − XM993 5′-GGTGAATTCGTTTTATTTCCCTCCGGGC-3′ ORF1b, −53 to −35 upstream of ORF2 + XM992 5′-GGGGGATCCTGTTGGTAATAG/AGTCTG-3′ ORF3, −50 to −34 upstream of ORF4 − XM970 5′-GGTTTCACCTAGAATGGC-3′ ORF2, 522 to 550 downstream of ORF2 + XM969 5′-GATAGAGTCTGCCCTTAG-3′ ORF5, 443 to 460 downstream of ORV6 − XM1006 5′-GCTTCTGAGATGAGTGA-3′ ORF4, 316 to 332 downstream of ORF4 + XM078 5′-CTGAGCAATTACAGAAG-3′ ORF2, 202 to 218 downstream of ORF2 + XM077 5′-CAACCAGGCGTAAACACT-3′ ORF3, 316 to 333 downstream of ORF3 − XM755 5′-GACTGCTTTACGGTCTCTC-3′ Leader, 3′end of the Leader sequence + 0P586 5′-GATGCCTGACACATTGCC-3′ ORF4, 355 to 372 downstream of ORF4 − XM141 5′-CTGCAAGACTCGAACTGAA-3′ ORF4, 78 to 97 downstream of ORF4 − ^(a)The oligonucleotides were designed on the basis of sequence data presented in this application and U.S. application Ser. Nos. 08/131,625 and 08/301,435 ^(b)Oligonucleotides complementary to the genomic RNA have negative (−) polarities.

EXAMPLE 3

Cell line ATCC CRL 11171 was used for the propagation of PRRSV isolates. The maintenance of the cell line and isolation of virus were the same as previously described (Meng et al., J. Gen. Virol. 75:1795-1801 (1994); Meng et al., J. of Veterinary Diagnostic Investigation 8:374-381 (1996). Plasmacytoma cell line SP2/O was used for cell fusion in MAb preparation. PRRSV ATCC VR 2385 was used as antigen for screening of hybridomas secreting PRRSV specific monoclonal antibodies.

Indirect Immunofluorescence Assay (IFA). Monolayers of ATCC CRL 11171 cells were inoculated with PRRSV VR 2385 at 0.1 multiplicities of infection, incubated for 48 hrs and fixed with methanol. Hybridoma supernatant was incubated on the fixed-cell monolayer at 37° C. for 30 min. Fluorescein-labeled goat anti-mouse IgG (H+L) conjugate was used to detect the specific reaction. One PRRSV N(ORF 7 products) specific monoclonal antibody, PP7eF11 was used as a positive control and cell culture supernatant from a non-PRRSV specific MAb, PPAc8 was used as a negative control.

MAb preparation. The whole cell lysates from insect cells infected with recombinant baculoviruses of PRRSV ORFs 4 and 5 were used as immunogen to immunize mice. Construction of the recombinant baculoviruses containing the PRRSV ORFs 4 and 5 was done with the strategies as previously described (Bream et al. J. Virol. 67:2665-2663 (1993)). Briefly, PRRSV ORFs 4 and 5 genes were PCR amplified separately from the template of pPSP.PRRSV2-7 plasmid (Morozov et al., Archives of Virology 140:1313-1319 (1995)) with primers containing restriction sites of BamHI and EcoRI. The amplified fragments were cut with the restriction enzymes indicated above and ligated into the vector PVL1393 (Invitrogen). The inserted genes were under control of the polyhedrin gene promoter (O'Reilly et al., Baculovirus Expression Vectors: A Laboratory Manual, pages 107-234, 2^(nd) Edition, New York: W.H. Freeman and Company (1992)) and verified with restriction enzyme digestion and PCR amplification. Then the recombinant vector DNA and linearized Autographa California multinuclear polyhedrosis virus DNA (Invitrogen) were co-transfected into Sf9 cells as described in the instruction manual. The inserted genes in the recombinant baculoviruses were verified with hybridization and PCR amplification (O'Reilly et al., 1992). The recombinant viruses were used to inoculate insect cells and the cell lysate was used for immunization of mice. The immunization was carried out with 3 to 5 times of intraperitoneal injections at two weeks interval. Spleenocytes were hybridized with SP2/O myeloma cells as previously described (Brown & Ling, “Murine Moncolonal Antibodies,” In Antibodies: a practical approach, pp. 81-104, Edited by Catty D. Zoxford, Washing, D. C. IRL Press (1988)). Hybridomas were screened for secreting PRRSV specific antibodies with IFA to detect reaction with PRRSV ATCC VR 2385. Positive hybridomas were selected and cloned three times. Four MAbs were developed to the GP4 and six Mabs to the protein. Mabs were isotyped with MonoAb ID kits (Zymed Laboratories Inc).

Enzyme-linked immunosorbent assay (ELISA). ELISA has been well described (Harlow & Lane, Antibodies: A laboratory manual, pp. 471-612, Cold Spring Harbor Laboratory New York (1988); Ausubel et al., Short protocols in molecular biology, pp. 11.5-11.7, 2^(nd) Edition, New York, Greene Publishing Associates and John Wiley & Sons (1992)). Coating antigens were extracted with 1% Triton X-100 from PRRSV VR 2385-infected cells. MAbs were tested for binding activity in ELISA with the antigens binding to plates. Extract from normal cells and cell culture medium from the non-PRRSV specific MAb, PPAc8 were included as a negative antigen and a negative antibody controls respectively. The PRRSV N-specific MAb, PP7eF11 was used as a positive control. Specific reactions were detected with goat anti-mouse IgG (H+L) peroxidase conjugate and revealed with substrate 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS). Then the optical density was measured at 405 nm (A₄₀₅).

Fixed-cell ELISA was conducted as previously reported (van Nieuwstadt et al., J. Virol. 70:4767-4772 (1991)) to test the reactivity of MAbs with PRRSV field isolates. Briefly, monolayers of ATCC CRL 11171 cells were inoculated with PRRSV field isolates at 0.001 multiplicities of infection, incubated for 48 hrs and fixed with methanol. Then the cells were blocked with 1% BSA for 1 hour at room temperature. Cell culture supernatant of MAbs were diluted in two-fold series and added to the fixed-cell plates. The PP7eF11 and PPAc8 were used as positive and negative controls respectively. Specific reactions were detected as described above.

Immunoblotting. Western immunoblot analyses were carried out as described previously (Harlow & Lane, Antibodies: A laboratory manual, pp. 471-612, Cold Spring Harbor Laboratory, New York (1988)). Protein samples were treated under different conditions before separated in gel. For denaturing conditions samples were treated at 100° C. for 3 minutes in Laemmli sample buffer containing 2% SDS and 5% 2-mercaptoethanol and run in SDS-PAGE. Under non-denaturing conditions, samples were treated at 40° C. for 20 min in sample buffer containing 1% triton X-100 and run in PAGE. Then separated proteins were transferred to nitrocellulose membrane by electrophoresis The nitrocellulose membrane was blocked with 3% BSA. MAbs were screened for the reactivity with the antigens on the membrane with multi-screening apparatus. Pig anti-PRRSV serum was used as a positive control and cell culture supernatant from PPAc8 as a negative control. Bound antibodies were detected by incubation with goat anti-mouse IgG+IgA+IgM peroxidase conjugate or goat anti-pig IgG peroxidase conjugate followed by color development in 4-chloro-1-naphthol substrate.

Virus neutralization (VN) test. Virus neutralizing activity of MAbs was tested as described previously (Mecham et al., Viral Immunol. 3:161-170 (1990) & White et al., J. Gen. Virol. 71:4767-4772 (1990)) with some modifications. Hybridoma supernatant was mixed with the same volume of PRRSV dilution containing 30-70 plaque forming units, which was diluted with DMEM containing 10% guinea pig complement. The virus-antibody mixture was incubated at 37° C. for 1 hr, and then transferred to the monolayer of ATCC CRL 11171 cells in six-well plate for 1 more hr incubation at 37° C. Then an agarose-medium mixture overlaid the monolayer. After 3-day incubation at 37° C., the monolayer was stained with 0.05% neutral red in agarose. Pig anti-PRRSV serum was used as a positive control and hybridoma cell culture medium from a non-PRRSV specific MAb was included as a negative control.

PRRSV specific Mabs identified with IFA. Hybridomas were screened with IFA on PRRSV VR 2385-infected ATCC CRL 11171 cells. IFA positive hybridomas were selected, amplified and cloned. Six MAbs were developed against PRRSV E protein and four to the GP4. All of them showed strong perinuclear fluorescence with a little difference in intensity, which was different from the cytoplasmic staining of PRRSV N protein specific MAb (FIG. 10). This result indicated that the GP4 and E glycoproteins were synthesized and accumulated in subcellular compartments in PRRSV-infected cells as transferring of oligosaccharides to a glycoprotein is generally processed in a particular compartment such as the endoplasmic reticulum and the Golgi complex (Pfeffer et al., Ann. Rev. Biochem. 56:829-852 (1987)). GP4 and E were predicted as membrane-associated glycoproteins (Meng et al., 1994 & Morozov et al., Archives of Virology 140:1313-1319 (1995)). In contrast, the PRRSV N protein is highly basic and hydrophilic, and is synthesized in the cytoplasm of PRRSV-infected cells, which was shown by the observation of cytosol distribution of fluorescence in IFA with N-specific MAb staining. All the MAbs were identified as subtype IgM.

Reactivity with PRRSV antigen in ELISA. In order to determine the sensitivity of the epitopes to detergent treatment, ELISAs were run to test the reactivity of the MAbs with 1% Triton X-100 extracted PRRSV antigen. Among the MAbs to the E protein, only PP5bH4 showed strong reactivity to the PRRSV antigen (FIG. 11). No clear reaction was detected between the rest of the E-specific MAbs and the PRRSV antigen. Among the MAbs to the GP4, only PP4bB3 showed a mild reactivity with the PRRSV antigen. The other three of the MAbs to GP4 failed to show any reactivity. The negative controls did not show reaction in ELISA.

Out of the 10 MAbs, only PP5bH4 and PP4bB3 showed reactivity in the ELISA with detergent extracted PRRSV antigen. This result indicated that the epitope recognized by PP5bH4 was resistant to Triton X-100 treatment and the epitope of PP4bB3 was partially resistant to the detergent. The epitopes recognized by the other 8 MAbs were sensitive to the treatment, and may be conformationally dependent. Triton X-100 is generally selected to disrupt cell membranes for its nondenaturing property (Deutscher, “Guide to protein purification,” Methods in Enzymology, Vol. 182, San diego, Calif., Academic Press, Inc. (1990)), but in this test the epitopes in the PRRSV proteins were somehow altered during the extraction process as monitored by the MAb binding.

Immunoblotting assay. Western-blotting was carried out to determine the reactivity of the MAbs with PRRSV antigen to confirm the speculation that the MAbs were against conformationally dependent epitopes. Under denatured conditions in SDS-PAGE, only the PP5bH4 recognized a band of purified PRRSV virions in the position of 26 kDa which corresponded with the putative E detected with pig anti-PRRSV serum (FIG. 12). Then immunoblotting was carried out with non-denatured PAGE to test if the epitopes were preserved under nondenaturing conditions. Among the six MAbs to E, only PP5bH4 showed reaction with the PRRSV antigen. Of the MAbs to GP4, none recognized the PRRSV antigen in purified virions or in infected cells under either conditions in this test (result not shown).

The MAbs except PP5bH4 failed to recognize the PRRSV antigen in immunoblot, which indicated that the epitopes recognized by these MAbs were not derived from continuous structure. MAb PP5bH4 reacted with PRRSV in the position of 26 kDa, which confirmed the report about the molecular mass of E (Meulenberg et al., Virology 192:62-72 (1995)). This result showed that the epitopes recognized by the other 9 MAbs were sensitive to detergent treatment and corresponded to that of ELISA. Again the result indicated that the epitopes were conformationally dependent. PP4bB3 failed to show any reaction with PRRSV antigen in Western-blot, which could be due to the epitope loss or alternation during PAGE and transfer.

Virus neutralizing activity. Plaque-reduction assay was run to test whether there was any virus neutralizing activity among the MAbs to the E and GP4 proteins. Only one E-specific MAb, PP5 dB4 showed the ability of homologous neutralization to the VR 2385 isolate. All the other MAbs failed to show any neutralizing activity to this isolate. The positive control, pig anti-PRRSV serum also showed virus neutralizing activity.

Among the ten MAbs to GP4 and E, at least PP5 dB4 showed homologous virus neutralizing activity against PRRSV VR 2385. The neutralizing epitope was conformationally dependent as PP5 dB4 failed to recognize PRRSV antigen in ELISA and in Western-blot. Also the neutralizing activity of PP5 dB4 indicates that at least part of the epitope is located on the virion surface and accessible by the MAb. The mechanism of neutralizing activity of PP5 dB4 is not clear. It could be due to blocking of the virus binding or entry into the cells.

Reactivity with other PRRSV isolates. PRRSV field isolates were propagated to test the cross-reactivity of the MAbs in fixed-cell ELISA and to determine the epitope presence in other PRRSV isolates (Table 5). Fixed-cell ELISA was used because most of these MAbs recognized conformationally dependent epitopes and these epitopes could be preserved in fixed cells. All the MAbs react with all the isolates but with different titers. The result indicates that the epitopes recognized by the MAbs were conserved among the isolates tested. However, there were antigenic differences among the isolates tested. Reactivity intensity was arbitrarily defined as high if titers were greater than or equal to 256, as medium if titers were 64 to 128, and as low if titers were smaller than or equal to 32. Out of the 23 isolates tested, only PRRSV VR 2385 had high reactivity with 7 of the 10 MAbs. Five isolates had low reactivity with at least 6 of the 10 MAbs, 12 isolates had medium reactivity with at least 6 of the 10 MAbs and the other 5 isolates had low reactivity with half of the MAbs. The MAb PP4dG6 and PP5bH4 showed lower reactivity with most of the isolates than other MAbs. The PP4bB3 showed the strongest reactivity among all the MAbs against GP4 and E proteins. The titer difference was as high as 64-fold for the reaction of one MAb with the different isolates, such as the titers of MAb PP4cBl 1 reacting with PRRSV RP 10 and RP 12, 16 and 1024 respectively. On the other hand, the titer difference of MAbs with one isolate was as high as 128-fold, such as the titers of MAbs PP4bB3 and PP4bC5 reacting with PRRSV RP11, 1024 and 8 respectively. This result indicated that the epitopes recognized by the different MAbs were different. The positive MAb control show strong reactivity with all the isolates except the ISU-51. The reactivity difference of MAbs with PRRSV isolates was consistent with the report that the amino acid sequence identity of VR 2385, ISU22, ISU55 and RP45 was 94-98% in ORF 4 and 88-97% in ORF 5 (Meng et al., J. Gen. Virol. 140:745-755 (1995)).

In summary, six MAbs were developed to the PRRSV E protein and four to the GP4. All of them except PP5bH4 were against conformationally dependent epitopes as determined by ELISA and immunoblotting. MAb PP5 dB4 showed virus neutralizing activity against VR 2385. Reactivity pattern of the MAbs with PRRSV field isolates indicated that there are antigenic difference in PRRSV GP4 and E, which confirmed previous reports on MAbs against PRRSV N and ORF 3 product (Nelson et al., J. Clinical Microbiology 31:3184-3189 (1993); Drew et al., J. General Virol. 76:1361-1369 (1995); Wieczorek-Krohmer et al., Veterinary Microbiology 51:257-266 (1996)).

EXAMPLE 4

Cells and viruses. ATCC CRL11171 cells were used to propagate PRRSV and PRRSV purification was done as previously described (Meng et al., J. Gen. Virol., 75:1795-1801(1994); Meng et al., J. Vet. Diag. Invest. 8:374-381(1996); Halbur et al. Vet. Pathol. 32:648-660, (1995). PRRSV isolate ATCC VR 2385 (Meng et al., 1994 & Morozov et al., 1995) was used for PCR amplification of ORFs 2 to 4 genes.

Spodoptera frugiperda clone 9 (Sf9) and High Five™ (Invitrogen) insect cells were cultured for propagation of baculovirus. The baculovirus strain Autographa California multinuclear polyhedrosis virus (AcMNPV) was used as parent virus for recombinant baculovirus construction.

Construction of AcMNPV recombinant transfer vector. Construction of the baculovirus transfer vectors containing the PRRSV ORFs 2, 3 and 4 separately was done with the strategies as previously described (Bream et al., J. Virol. 67:2655-2663(1993). Briefly, PRRSV ORFs 2 to 4 genes were PCR amplified separately from the template of pPSP.PRRSV2-7 plasmid with primers containing restriction sites of BamHI and Pst I for genes of ORFs 2 and 3, BamHI and EcoRI for ORF 4.

The forward primer for ORF 2 was 5′GCACGG ATCCGAATTAACATGAAATGGGGT3′ and the reverse primer was 5′CCACCT GCAGATTCACCGTGAGTTCGAAAG3′. The forward primer for ORF 3 was 5′CGTCGGATCCTCCTACAATGGCTAATAGCT3′ and the reverse primer was 5′CGCGCTGCAGTGTCCCTATCGACGTGCGGC3′. The forward primer for ORF 4 was 5′GTATGGATCCGCAATTGGTTTCACCTATAA 3′ and the reverse primer was 5′ATAGGAATTCAACAAGACGGCACGATACAC3′. The amplified fragments were cut with restriction enzymes as indicated above and ligated into the vector pFastBAC1 (GIBCO BRL) for ORFs 2 and 3 fragments, and the vector PVL1393 (Invitrogen) for ORF 4 fragment. The inserted genes were under control of the polyhedrin gene promotor (O'Reilly et al., Baculovirus Expression Vectors: A Laboratory Manual, W.H. Freeman & Co., NY (1992) and verified with restriction enzyme digestion and PCR amplification. Then the recombinant vectors containing the ORFs 2 to 4 genes separately were isolated and designated as pPSP.Ac-p2 for ORF 2 transfer vector, pPSP.Ac-p3 for ORF 3 transfer vector and pPSP.Ac-p4 for ORF 4 transfer vector. For pPSP.Ac-p2 and pPSP.Ac-p3, their DNA were isolated and transfected into competent DH10BAC E. Coli cells (GIBCO BRL) containing the whole genome of baculovirus called Bacmid.

Transfection and selection of recombinant viruses. For ORFs 2 and 3, recombinant viruses were generated with the BAC-TO-BAC™ expression system (GIBCO BRL). The isolated recombinant Bacmid DNA were transfected into Sf9 insect cells and then the cell culture medium was collected as virus stock. For ORF 4 recombinant virus construction, pPSP.Ac-p4 DNA and linearized AcMNPV DNA (Invitrogen) were co-transfected into Sf9 cells as described in the instruction manual. Putative recombinant baculoviruses were selected following three rounds of occlusion body-negative plaque purification. The inserted genes in the recombinant viruses were verified with hybridization and PCR amplification (O'Reilly et al., 1992). Four recombinants were selected for each of the 3 strains of recombinant baculoviruses. Indirect immunofluorescence assays with pig anti-PRRSV serum showed that the four recombinants for each strain had similar level of protein expression. One was chosen from each strain for further study and designated as vAc-P2 for recombinant virus of ORF 2, vAc-P3 for that of ORF 3, and vAc-P4 for that of ORF 4.

Indirect Immunofluorescence Assay (IFA). IFA was well described elsewhere (O'Reilly et al., 1992). Briefly, Monolayer of High Five™ cells were infected with wild type (wt) AcMNPV or recombinant viruses of vAc-P2, vAc-P3 and vAc-P4 respectively at a multiplicity of infection of 0.1 and incubated for 72 hrs. Pig anti-PRRSV serum was used to detect specific proteins expressed in insect calls. Total protein expression was detected in the infected cells fixed, stained and observed under fluorescence microscope. Cell surface expression was detected on unfixed and unpermeabilized cells incubated with pig anti-PRRSV serum for 1 hr at 4° C., stained with fluorescein-labeled goat anti-pig IgG conjugate for 1 hr at 4° C., and then observed under fluorescence microscope.

Immunoblotting. Western immunoblotting was conducted as previously described (Harlow & Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory (1988)). Cell extract from insect cells infected with recombinant viruses or wt AcMNPV were used for this analysis. The proteins were separated with SDS-PAGE and transferred to nitrocellulose membrane by electrophoresis. The membrane was incubated with pig anti-PRRSV serum for 1 hour at room temperature. Specific reactions were detected with goat anti-pig IgG peroxidase conjugate, followed by color development in 4-chloro-1-naphthol substrate.

Tunicamycin treatment. High Five™ cells were infected with vAc-P2, vAc-P3, vAc-P4 or wt AcMNPV and incubated with 5 μg/ml tunicamycin in cell-culture medium from 0 to 72 hrs post infection. Non-treated insect cells were infected at the same time as controls. Cell lysate was harvested for SDS-PAGE and immunoblotting (O'Reilly et al., 1992).

Immunogenicity of the recombinant proteins. Cell lysates of insect cells infected with vAc-P2, vAc-P3 and vAc-P4 were used to test the recombinant protein's immunogenicity in rabbits. Two twelve-week old rabbits were injected intramuscularly and subcutaneously for each of these recombinant proteins. Blood was collected 10 days after two booster injections. Antibodies were tested with indirect ELISA (Ausubel et al., Short Protocols in Molecular Biology, pp. 11.5-11.7, 2^(nd) Edition, N.Y. Green Publishing Associates and John Wiley and Sons (1992)). Purified PRRSV virions were sonicated and used to coat 96-well plates and goat anti-rabbit IgG peroxidase conjugate was used to detect anti-PRRSV antibodies in rabbit serum samples. Pre-immune rabbit serum was used as negative control. Substrate 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) was used to reveal specific reactions.

Results

Construction and verification of recombinant viruses. Details of construction strategy are mentioned under Methods. For ORFs 2 and 3, the recombinant baculoviruses were selected from E. coli containing the recombinant Bacmid and then collected from transfection of Sf9 insect cells. The recombinant viruses were further confirmed by DNA hybridization and PCR amplification. Both hybridization of DNA from infected cells with specific probes from the PRRSV genes of ORFs 2 to 4 and PCR amplification showed that the recombinant baculoviruses had the right genes cloned (data not shown).

Surface immunofluorescence of recombinant viruses vAc-P2, vAc-P3 and vAc-P4. High Five™ cells were infected with vAc-P2, vAc-P3, vAc-P4, or wt AcMNPV, incubated for 72 hrs, and fixed with methanol for examination of total protein expression by IFA with pig anti-PRRSV serum. Unfixed and unpermeabilized insect cells were stained at 4° C. to detect cell surface immunofluorescence by IFA. There was weak cytoplasmic fluorescence in vAc-P2 infected cells, intense cytoplasmic fluorescence in vAc-P3 or vAc-P4 infected insect cells and no specific fluorescence in wt AcMNPV infected cells (FIG. 17). There was clear cell surface immunofluorescence in vAc-P2, vAc-P3 and vAc-P4 infected insect cells stained at 4° C. without fixation and permeabilization (FIG. 15). No cell surface staining was detected in wt AcMNPV infected insect cells. Also, recombinant virus infected insect cells in the absence of antibody did not show any fluorescence (data not shown).

Analysis of expressed recombinant proteins. Monolayer of High Five™ cells was infected at a multiplicity of infection of 0.1 with vAc-P2, vAc-P3, vAc-P4, or wt AcMNPV and incubated for 72 hrs. Expression of the recombinant proteins in insect cells was analyzed with whole cell extracts. Total protein samples were run on SDS-PAGE, transferred to nitrocellulose membrane by western-blotting and detected with pig anti-PRRSV serum (FIG. 19A). Purified PRRS virions were added and analyzed in the same gel. The ORF 2 product expressed in insect cells was detected as 27 and 29 kDa bands in M_(r). The ORF 3 product was detected as 22, 25, 27-31 and 3543 kDa multi-band species. The signals in M_(r) of 27-31 and 35-43 kDa were hard to differentiate into single bands and may be due to differential glycosylation or partial proteolysis. The ORF 4 product was found as 15, 18, 22, 24, 28 and 30 kDa multi-band species. These specific bands were not detected in wt AcMNPV infected insect cells. There were at least four bands in purified PRRSV sample: 15, 19, 27-31 and 45 kDa in M_(r). The specific bands detected in purified PRRS virions were not observed in normal cell control (FIG. 19A).

The recombinant proteins were glycosylated. Tunicamycin treatment of insect cells infected with recombinant baculoviruses or wt AcMNPV was conducted to test if the recombinant proteins were N-glycosylated as tunicamycin inhibit N-linked glycosylation. After the treatment, the 29 kDa band of the ORF 2 recombinant protein was disappeared, a 25 kDa appeared and the 27 kDa species remained unchanged (FIG. 20A). For the ORF 3 recombinant protein, the species of 27-31 and 35-43 kDa were disappeared and the 22-27 kDa bands remained unchanged. The 27 kDa species of ORF 3 recombinant protein became more abundant after tunicamycin treatment. After the N-glycosylation inhibition, the ORF 4 recombinant protein was shown as 15 and 18 kDa species only and the bands of 22-30 kDa were disappeared. The 15 and 18 kDa bands became sharper and darker after the tunicamycin treatment. No signal was detected in extracts from wt AcMNPV infected insect cells.

Immunogenicity of the recombinant proteins. The recombinant proteins of ORFs 2 to 4 products were tested for immunogenicity by immunization of rabbits with lysates of insect cells infected with vAc-P2, vAc-P3 and vAc-P4. The presence of anti-PRRSV antibodies in the rabbit serum samples was detected by ELISA. The average titers of immunized rabbits were 192, 128 and 382 for the groups of vAc-P2, vAc-P3 and vAc-P4 cell lysate respectively (Table 6).

Discussion

The genes of ORFs 2 to 4 of PRRSV were cloned into BEVS and the recombinant proteins were expressed in insect cells. The cloning strategy for ORFs 2 and 3 was much faster than that for ORF 4 as the selection process of recombinant baculovirus was done in E. Coli instead of choosing occlusion body-negative plaques on Sf9 cells. Sf9 cells were used for the propagation of baculovirus, and High Five™ cells were used for protein expression as protein yield in High Five™ cells was believed to be higher than that in Sf9 cells (Wickham et al. Biotechnology Progress 8:391-396 (1992) & Davis et al., In Vitro Cell and Developmental Biology 29A: 388-390 (1993)). The High Five™ cells were adapted to serum free medium, which benefits for future protein purification, and can be adapted to suspension culture, which is suitable for large scale industrial production.

The recombinant proteins were shown by IFA to express in insect cells infected with vAc-P2, vAc-P3 and vAc-P4 recombinant viruses. There was weak cytoplasmic fluorescence in vAc-P2 infected cells, strong cytoplasmic fluorescence in vAc-P3 and vAc-P4 infected cells. The reason for the weak fluorescence of vAc-P2 infected cells is not known and could be due to epitope alternation after fixation with methanol. The unfixed and unpermeabilized insect cells were stained at 4° C. to make sure that the pig anti-PRRSV antibody reacted with cell surface proteins only and did not enter into cytoplasm. There was clear cell surface immunofluorescence on the insect cells infected with vAc-P2, vAc-P3 or vAc-P4, which indicates that the recombinant proteins were efficiently processed and transported to cell surface. This result indicates that ORFs 2 to 4 products are membrane-associated proteins, which is consistent with the predictions from sequence studies (Morozov et al., Archives of Virology 140:1313-1319 (1995)). However, it is not clear if these products are also transported to cell surface of PRRSV infected mammalian cells or assembled into virions as surface proteins. Recent report showed that the ORFs 3 and 4 products are viral structural proteins (VAN Nieuwstadt et al, J. Virol. 70:4767-4772 (1996)). Further experiment is needed to investigate the destiny of these proteins.

Immunoblotting results showed that the recombinant proteins were efficiently expressed in insect cells. The ORF 2 product was detected as 27 and 29 kDa species in M. Tunicamycin treatment eliminated the 29 kDa band and introduced the 25 kDa species with the 27 kDa unchanged, which indicated that the 29 kDa was N-glycosylated. The predicted M, of PRRSV VR 2385 ORF 2 is 29.5 kDa with two potential glycosylation sites (Morozov et al., 1995). The 25 kDa species may be the core protein of ORF 2 if the 37-38 signal sequence (Meulenberg et al., Virology 192:62-72 (1995)) are removed in the mature protein. The 4 kDa difference between the 29 and 25 kDa bands may be due to carbohydrate structures as one glycosyl moiety has a M_(r) of about 2-3 kDa (Trimble et al., J. Biol. Chem. 250:2562-2567 (1983)). The 27 kDa species was not sensitive to the tunicamycin treatment and may be modified by 0-linked glycosylation or other post-translational modifications.

The ORF 3 product in insect cells was shown as 22-43 kDa multi-band species detected by immunoblotting. The 28-43 kDa species were eliminated by tunicamycin treatment of vAc-P3 infected insect cells, which indicated that they were N-linked glycoproteins and the multi-bands were due to differential glycosylation. The predicted Mr of PRRSV VR 2385 ORF 3 product is 28.7 kDa (about 2 kDa less than the counterpart of LV) with 7 potential N-linked glycosylation sites (Morozov et al., 1995). The 27 kDa species of ORF 3 recombinant protein may be the core protein because it became more abundant after tunicamycin treatment (FIG. 20A) and because a 27 kDa band appeared and a 45 kDa band disappeared after endoglycosidase F treatment of purified PR RSV virion (data not shown). The species smaller than 27 kDa may be truncated proteins or products of proteolysis. The 27-43 kDa bands in nontreated sample are hard to differentiate into individual bands, which may be due to overloading or partial proteolysis. The 43 kDa species may be the fully glycosylated product as there are 7 N-linked glycosylation sites and about 2-3 kDa are counted for each glycosyl moiety (Trimble et al., 1983). The recent report showed that ORF 3 of LV encode a 45-50 kDa structural protein and that recombinant proteins of ORF 3 in insect cells were detected as 28-44 kDa in M, by radioimmunoprecipitation (VAN Nieuwstadt et al., 1996). The 28 kDa species was found as the core protein of LV ORF 3 product. It seems there is difference in Mr of recombinant proteins from ORF 3 of US PRRSV and LV, which may be due to the different expression system used or the difference in this gene between the two isolates. Another report showed that the recombinant fusion protein of carboxyterminal 199 amino acids of LV ORF 3 expressed in baculovirus was not N-glycosylated (Katz et al., Vet. Microbiol. 44:65-76 (1995)), which demonstrates the diversity of expressed products from the same gene.

The ORF 4 product in insect cells was detected as 15-30 kDa multi-band species. After tunicamycin treatment the 22-30 kDa bands were eliminated and the 15, 18 kDa bands remained unchanged, which indicated that the 22-30 kDa species were N glycosylated to various degrees. The ORF 4 of PRRSV VR 2385 was predicted to encode a 19.5 kDa protein with 4 potential N glycosylation sites (Morozov et al., 1995). The 15 kDa species of ORF 4 product may be the core protein and the 18 kDa band may be the core protein plus 0-linked glycosyl moiety or other modifications. It was reported that LV ORF 4 encoded a 31-35 kDa structural protein and that the recombinant protein of ORF 4 expressed in insect cells was detected as 20-29 kDa species with a 17 kDa core protein (VAN Nieuwstadt et al., 1996). Again, the reason for the difference in Mr may be due to the cloned gene's difference and the different expression systems. Another report demonstrated the difference by showing that ORF 4 is not a well conserved region (Kwang et al., J. Vet. Diag. Invest. 6:293-296 (1994)).

The immunization of rabbits with the recombinant proteins showed that they had induced anti-PRRSV antibodies. This result indicates that these recombinant proteins may have the similar immunogenicity as their native counterparts in PRRSV infected mammalian cells.

This study showed that the ORFs 2 to 4 of PRRSV VR 2385 were expressed in BEVS and detected both in cytoplasm and on cell surface of insect cells. The recombinant proteins of ORFs 2 to 4 were N-linked glycoproteins with differential glycosylation. The purified PRRSV virions were analyzed as the same time and showed 4 bands in immunoblotting. But due to lack of oligoclonal or monoclonal antibodies it is hard to tell if any of ORFs 2 to 4 products was detected in the purified virions. The reaction of pig anti-PRRSV serum with the recombinant proteins indicated that the native counterpart of these proteins induced immune response in natural host. The induction of anti-PRRSV antibodies in rabbits indicated that these recombinant proteins had similar immunogenicity as the native ORFs 2 to 4 products in PRRSV infected natural host. TABLE 6 Rabbit antiserum titers tested with ELISA Groups of insect cells infected with Number of rabbits Means of titers* vAc-P2 2 192 vAc-P3 2 128 vAc-P4 2 384 *Titers were expressed as the reciprocals of the highest dilutions shown positive in ELISA.

EXAMPLE 5

Cells and viruses. ATCC CRL11171 cells were used to propagate PRRSV (Meng et al., 1994 and 1996; Halbur et al., 1995). Spodoptera frugiperda clone 9 (Sf9) and High Five™ (Invitrogen) insect cells were used for propagation of baculovirus. PRRSV isolate VR 2385 (Meng et al., 1994 and 1996) was used for gene amplification and cloning into BEVS. PRRSV virions were purified as previously described (Meng et al., 1994). The baculovirus strain Autographa California multinuclear polyhedrosis virus (ACMNPV) was used as parent virus for recombinant virus construction.

Construction of ACMNPV recombinant transfer vector. The nucleic acid sequence of the ORFs 5-7 of PRRSV VR2385 was previously described (Meng et al. 1994). Construction of the baculovirus transfer vectors containing the PRRSV ORFs 5 to 7 separately was done with the strategies as described previously (Bream et al. 1993). Briefly, PRRSV ORFs 5 to 7 genes were PCR amplified separately from the template pPSP.PRRSV2-7 plasmid with primers containing restriction sites of BamHI and EcoRI. The forward primer for ORF5 was 5′TGCCAGGATCCGTGTTTAAATATGTTGGGG3′ and the reverse primer was 5′CGTGGAATTCATAGAAAACGCCAAGAGCAC3′. The forward primer for ORF6 was 5′GGGGATCCAGAGTTTCAGCGG3′ and the reverse primer was 5′GGGAATCCTGGCACAGCTGATTGAC3′. The forward primer for ORF7 was 5′GGGGATCCTTGTTAAATATGCC3′ and the reverse primer was 5′GGGAATTCACCACGCATTC3′. The fragments amplified were cut with BamHI and EcoRI, isolated and ligated into vector PVL1393 (Invitrogen) which was also cut with BamHI and EcoRI to insure correct orientations. The inserted genes were under control of the polyhedrin gene promotor (O'Reilly et al., 1992) and verified with restriction enzyme digestion and PCR amplification. The recombinant vectors containing the ORFs 5 to 7 genes separately were isolated, pPSP.Ac-E for ORF5, pPSP.Ac-M for ORF6 and pPSP.Ac-N for ORF7 transfer vectors.

Transfection and selection of recombinant viruses. Sf9 insect cells were cotransfected with linearized AcMNPV DNA (Invitrogen) and recombinant plasmid DNA of pPSP.Ac-E, pPSP.Ac-M, and pPSP.Ac-N respectively as per manufacturer's instructions. Putative recombinant viruses were selected following three-round of purification of occlusion-negative plaques. The inserted genes in the recombinant viruses were verified with hybridization and PCR amplification (O'Reilly et al., 1992). Four recombinants were selected for each of the 3 strains of recombinant viruses and were found to be similar in immunofluorescence assays using pig anti-PRRSV serum. One recombinant virus was chosen arbitrarily from each strain and designated as vAc-E1 for recombinant virus containing ORF5, vAc-M1 for that with ORF6, and vAc-N1 for that with ORF7.

Immunoblotting. Western immunoblot analyses were carried out as described previously (Harlow and Lane, 1988). Whole proteins from infected insect cells, purified PRRSV or normal cells were used as samples. Proteins were separated with SDS-PAGE and transferred to nitrocellulose membrane by electrophoresis. The nitrocellulose membrane was blocked with 3% BSA and reacted with pig anti-PRRSV serum for 1 hour at room temperature. Bound antibodies were detected by incubation with goat anti-pig IgG peroxidase conjugate, followed by color development with 4-chloro-1-naphthol substrate.

Tunicamycin treatment. Infected High Five™ cells were incubated with 5 μg/ml tunicamycin in cell-culture medium from 0 to 72 hr post infection and harvested for SDS-PAGE (O'Reilly et al., 1992).

Cleavage with glycosidases. Endoglycosidase F/N-glycosidase F mixture (PNGase F) and endoglycosidase H (Boehringer-Mannheim Biochemicals) were used to treat lysates from infected High Five™ cells (0.1 PFU/cell; 72 hr post infection) in the case of recombinant proteins or purified PRRSV as per manufacturer's instructions. Briefly, 10⁵ cells were lysed with 30 μg lysis buffer. Then 10 μg of cell lysates was digested with PNGase F, endoglycosidase H or kept untreated and used as non-treated control. The samples were incubated at 37° C. for 24 hrs before analysis on SDS-PAGE.

Radioimmunoprecipitation (RIP). High Five™ cells infected with recombinant baculovirus or wild type (wt) AcMNPV and uninfected High Five™ cells were washed once with methionine-free medium and starved for one hour at 48 hr post-infection. Then 50 ci/ml Tran³⁵S-label (methionine and cystine) (Amersham Life Science Inc.) in methionine-free medium was added to the infected cells. Three hours later the cells were rinsed with PBS and laced in RIPA lysis buffer (10 mM Tris-HCl, pH8.0; 1 mM EDTA; 150 mM NaCl; 1% NP40; 1% sodium deoxycholate; 0.1% SDS). Immunoprecipitation and gel electrophoresis were performed as described previously (Hutchinson et al., J. Virol. 66:2240-2250 (1992).

Indirect Immunofluorescence Assay (IFA). IFA was conducted as previously described (O'Reilly et al., 1992). Monolayer of High Five™ cells were inoculated with wt AcMNPV or recombinant baculoviruses, incubated for 72 hrs and fixed to detect all recombinant protein expression with pig anti-PRRSV serum. The inoculated insect cells were also examined for the presence of cell surface proteins. Unfixed and unpermeabilized cells were reacted with the pig antiserum at 4° C. for 1 hr, incubated with fluorescein-labeled goat anti-pig IgG conjugate for 1 more hr at 4° C. and then observed under fluorescent microscope.

Immunogenicity of the recombinant proteins. Twelve-week old rabbits were injected intramuscularly and subcutaneouslly with lysates of insect cells infected with vAc-E1, vAc-M1 and vAc-N1. Two rabbits were immunized for each of E, M, and N recombinant proteins. Two booster injections were given in an interval of three weeks. The injection dose was cell lysates from 2×10⁶ insect cells. Blood was collected 10 days after the second booster injection. Antibodies were tested with indirect ELISA. Purified PRRSV virions were sonicated and used to coat 96-well plates and goat anti-rabbit IgG peroxidase conjugate was used to detect anti-PRRSV antibodies in rabbit serum samples. Pre-immune rabbit serum was used as negative control. Substrate 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) was used to reveal specific reactions.

Results

Confirmation for the presence of PRRSV gene in recombinant baculovirus. Hybridization and PCR amplification were performed to verify the presence the cloned genes in recombinant baculovirus. Hybridization of probes from the PRRSV genes with recombinant baculovirus showed that the PRRSV genes were present in the recombinant baculovirus. PCR amplification with specific primers from PRRSV genes showed single band from the recombinant virus and absent from the wt AcMNPV (results not shown). These tests confirmed that the recombinant baculoviruses contain the PRRSV genes ORFs 5 to 7. Surface immunofluorescence of recombinant viruses vAc-E1 and vAc-M1, but not vAc-N1. High Five™ cells infected with vAc-E1, vAc-M1, vAc-N1, and wt AcMNPV were examined for the presence of total expressed protein and cell surface expression. There was weak cytoplasmic fluorescence in vAc-E1 and vAc-M1-infected cells. In contrast, there was intense cytoplasmic fluorescence in vAc-N1-infected insect cells and no fluorescence in wt AcMNPV infected cells (FIG. 18). Clear cell surface immunofluorescence was detected in vAc-E1 and vAc-M1 infected insect cells (FIG. 16). However, there was no surface immunofluorescence in insect cells infected with vAc-N1 or wt AcMNPV. Also, in the absence of antibody insect cells infected with the recombinant viruses did not show any fluorescence (data not shown).

Analysis of ORFs 5-7 products expressed in insect cells. To analyze the expression of the expected proteins in insect cells, confluent monolayers of High Five™ cells were infected at a multiplicity of infection of 0.1 PFU/cell with vAc-E1, vAc-M1 and vAc-N1 respectively and incubated for 72 hr. Total protein samples were run on SDS-PAGE and analyzed by western-blotting using pig anti-PRRSV serum (FIG. 19A). The recombinant protein E expressed in insect cells was detected as multi-band species of 16, 18, 20, 24, and 26 kDa. The E expressed in insect cells showed more diversity and lower M_(r) compared with the native E, 26 kDa species, in the purified PRRSV (FIG. 19A). The M expressed in insect cells was detected as a 19 kDa band, which corresponded to the native M in purified PRRSV. The N expressed in insect cells was detected as a 15 kDa band, which also corresponded to the native N in the purified PRRSV. These specific bands were not detected in normal insect cells (results not shown) and those infected with wt AcMNPV. Purified PRRS virions were analyzed in the same gel. There were at least five bands: 15, 19, 24, 26-30 and 45 kDa. The specific bands detected in purified PRRS virions were not observed in normal mammalian cell controls.

Glycosylation analysis of baculovirus expressed E, M, and N. To determine if the E, M, and N expressed in insect cells underwent N-glycosylation, the insect cells infected with the recombinant baculoviruses were treated with tunicamycin to inhibit N-linked glycosylation. After tunicamycin treatment, the 20-26 kDa species were not detected in insect cells infected with the vAc-E1 (FIG. 20B), while the 16 and 18 kDa bands became more abundant. In the cells infected with vAc-M1 and vAc-N1, no changes in M_(r) of M and N proteins were detected after the tunicamycin treatment (FIG. 20B).

Immunogenicity of the recombinant proteins. The recombinant proteins E, M, and N were tested for immunogenicity by immunization of rabbits with lysates of insect cells infected with vAc-E1, vAc-M1 and vAc-N1. Then ELISA was carried out to test for the presence of anti-PRRSV antibodies in the rabbit serum samples. The average titers of E, M and N immunized rabbits were 384, 320 and 2,056 respectively (Table 7).

Discussion

Recombinant baculoviruses containing the genes E, M, and N of PRRSV were constructed to express E, M, and N in insect cells. Sf9 cells were used for the propagation of baculovirus, and High Five™ cells were used for protein expression as protein yield in High Five™ cells was believed to be higher than that in Sf9 cells (Wickham et al., 1992 and Davis et al., 1993).

Immunofluorescence analysis showed that E, M and N were expressed in insect cells infected with recombinant viruses containing those genes and showed that E and M were transported to the cell surface in insect cells. This result indicates that E and M expressed in insect cells are membrane-associated proteins and efficiently processed in post-translational modification. The reason for low intensity of cytoplasmic immunofluorescence of E and M in insect cells is unclear. It may be due to the epitope loss or modification after fixation of the infected insect cells. In insect cells infected with vAc-N1, only intense cytoplasmic immunofluorescence was observed and no surface fluorescence was detected. This result indicated that baculovirus expressed N was not transported to cell surface but located in the cytosol. This characteristic is consistent with its nature as a very hydrophilic nucleocapsid protein as predicated from sequence studies (Meng et al., 1994).

The recombinant E protein showed multi-bands in immunoblotting, the bands with M_(r) smaller than 26 kDa were not found in the purified PRRSV. The E expressed in insect cells showed more diversity and lower M_(r) compared with the native E, 26 kDa species, in the purified PRRSV (FIG. 19). The multi-bands may be due to differential glycosylation in insect cells during post-translational modification. Tunicamycin treatment eliminated the 20-26 kDa bands and increased the intensity of the 16 kDa band. The presence of the 18 kDa band after treatment could be due to 0-linked glycosylation, phosphorylation or other post-translational modifications. The 20-26 bands represent those of differential N-glycosylated species of E in insect cells. The 16 kDa band may be the non-glycosylated leader-free core protein. Preliminary studies of PNGase F and endoglycosidase H treatment of recombinant protein E showed that it underwent complex glycosylation. The recombinant M and N did not undergo N-linked glycosylation as both the tunicamycin and PNGase F and endoglycosidase H treatments did not alter the mobilities of the 19 and 15 kDa bands. These results indicate that the recombinant protein E of 20-26 kDa is N-glycosylated, and that the recombinant M and N proteins expressed in insect cells are not N-glycosylated. The changes in mobility after tunicamycin treatment were consistent with the presence of two N-linked glycosylation sites in the E polypeptide as determined from sequence studies (Meng et al., 1994). However, sequence studies indicated that there are 2 and 1 potential N-linked glycosylation sites in the M and N polypeptides respectively. In the baculovirus expressed M and N, there was no N-linked glycosylation detected. Compared with the native counterparts, the recombinant proteins in insect cells were much more abundant as seen from the immunoblot (the loading amount of the recombinant proteins was about one percent of the PRRSV lane in FIG. 19). However, it is difficult to measure the difference without oligoclonal or monoclonal antibodies.

For the purified PRRSV, there are at least five bands: 15, 19, 24, 26-30 and 45 kDa. This result is consistent with the previous reports that there are at least three structural proteins in the PRRSV virion (Conzelmann et al., Virology 193:329-339 (1993); Nelson et al., J. Clin. Microbiol. 31:3184-3189 (1994) and Mardassi et al., Arch. Virol. 140:1405-1418 (1994)). The 45 kDa band in the purified PRRSV may be the ORF3 product as reported (Kapur et al., J. Gen. Virol. 77:1271-1276 (1996)). The nature of the 24, 27-30 kDa species can not be figured out. After treatment with PNGase F and endoglycosidase H, the band pattern changed for the PRRSV sample. In the PNGase F treated PRRSV, the 16-kDa band may represent the non-glycosylated leader-removed core protein of E, the 27-kDa band may indicate another structural protein of PRRSV besides E, M and N. However, the nature of these bands needs to be determined by oligoclonal or monoclonal antibodies.

The results from rabbit immunization test indicated that the antibodies generated from the immunization of rabbits with the recombinant proteins could recognize the native PRRSV viral antigens. The recombinant proteins showed the same antigenicity as their native counterparts in PRRSV infected mammalian cells, especially the recombinant N which induced higher antibody titers in rabbits than did E and M. TABLE 7 Rabbit antiserum titers tested with ELISA Groups of insect cells infected with Number of rabbits Means of titers* vAc-E1 2 384 vAc-M1 2 320 vAc-N1 2 2056 *Titers were expressed as the reciprocals of the highest dilutions of serum that showed positive reading.

EXAMPLE 6

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), Modified Live Virus vaccine was prepared as a lyophilized viral cake and reconstituted with sterile water and administered by either the subcutaneous (SC) or intramuscular (IM) route. The objective of this study was to confirm the immunogenicity of a PRRSV vaccine in three week-old swine by vaccinating either IM or SC with one 2 mL dose. Also to be determined was whether the PRRSV vaccine was safe and efficacious in three week-old pigs vaccinated with a single 2 mL dose, given with IM or SC, in protecting pigs against challenge with virulent PRRSV strain ISU-12.

Animal Selection

Seventy crossbred PRRSV seronegative pigs (IDEXX ELISA sample to positive ratio of <0.4) were purchased from Evergreen Partners, Morris, Minn. and utilized in this study. All pigs were three weeks old at the time of vaccination.

Composition of the Vaccine

The PRRSV vaccine comprising virus strain ISU-55 was produced at virus passage level X+5. The vaccine was stored between 2°-7° C. prior to use. The vaccine was titrated in five replicates.

Vaccination Schedule—Efficacy Testing

The stock vaccine was prepared by reconstituting the lyophilized virus portion with sterile water. The stock vaccine was diluted to the minimum protective dose level (approximately 10⁴ TCID₅₀ per dose) in culture medium. A representative aliquot of the prepared vaccine was retained at −70° C. for quantitation of viral antigen. The 70 PRRSV seronegative susceptible pigs used in this study were randomly distributed into four treatment groups and vaccinated as follows: Group Vaccine Route Dose Number Vaccination Group A PRRSV IM 2 mL 20 pigs Vaccination at 3 vaccine weeks of age. Group B PRRSV SC 2 mL 20 pigs Vaccination at 3 vaccine weeks of age. Group C N/A* N/A N/A 20 pigs N/A (Controls) Group D N/A N/A N/A 10 pigs N/A (Controls) *N/A—Not applicable

Injection sites were in the right neck (IM) or in the right flank fold (SC). The control pigs (Groups C and D) were not vaccinated with any vaccine or placebo vaccine.

Prior to vaccination, all pigs were bled for a prevaccination serology. Control animals were bled prior to challenge to ensure that they remained seronegative to PRRSV (IDEXX ELISA S/P ratio<0.4).

Challenge and Observation Procedure

Thirty-six (36) days after the vaccination, each of the 20 pigs in Groups A, B and C were commingled in a common isolation room and challenged with virulent PRRSV. Group D animals were left as nonchallenged controls. The virulent ISU-12 PRRSV challenge virus was obtained from Iowa State University, Ames, Iowa. The virulent ISU-12PRRSV challenge virus was maintained as a frozen (−70° C.) stock after expansion in PSP36 cells. Individual pigs were challenged intranasally with 2 mL of the challenge virus. The PRRSV challenge stock was thawed and diluted to 10⁴ TCID₅₀ per 2 mL just before challenge. The challenge virus was held on ice during challenge. An aliquot of the challenge virus preparation was retained and held at −70° C. for subsequent titration on PSP36 cells. The animals were observed on −1, and 0 days post challenge (DPC) to establish a baseline and 1 to 10 DPC for various clinical signs.

Clinical Observation

The pigs were evaluated each day for post challenge clinical signs such as inappetence, lethargy, depression, diarrhea, neurological symptoms, dyspnea, cyanosis and death.

Lung Lesion Scoring

The lungs of each individual pig were examined for gross lesions at necropsy 10 days post challenge. The scorer of gross lung lesions was blinded to the identity of the treatment group to which each pig belonged. Briefly, the score for lung lesions in each lobe were recorded by estimating the percent of the lobe exhibiting PRRSV-like lesions (based on color and texture) and multiplied by the number of points possible for that lobe. Maximum score for each lobe was determined by the relative percentage of the total lung volume occupied by the lobe. Then the scores from the dorsal and ventral aspects of all lobes were added to obtain the total score for each pig. The maximum total score possible for each animal was 100.

Statistical Analysis

The clinical sign and gross lung lesion scores for the vaccinates and the controls were compared using analysis of variance (General Linear Model). The use of analysis of variance models using nonranked gross lung lesion scores was justified by the fit of the scores within a normal probability distribution. A comparison of the residuals of the parametric analysis indicated they were distributed normally, substantiating the major assumptions for analysis of variance. Therefore, data analysis using ranked gross lung lesion scores was not necessary. All statistical analyses were performed on an IBM computer using SAS software.

Results and Discussion

PRRSV Antigen Titers in the VS Code Vaccine

The PRRSV vaccine antigen titration results are shown in Table 8. The average PRRSV titer per dose of vaccine from five replicate titrations was 10^(3.92) TCID₅₀.

Clinical Observations

Following vaccination, there were no clinical signs observed in any of the vaccinated pigs. Following challenge with virulent PRRSV ISU-12 p6, the vaccinates and control pigs did not show significant clinical signs of respiratory or neurologic disease during the 10 day post challenge observation period.

Gross Lung Lesion Pathology

The results of gross lung lesion scoring are given in Table 9. Following PRRSV challenge, the gross lung lesion scores ranged from 0-29 with a mean score of 14.15 in the IM vaccinated pigs (Group A), from 1-27 with a mean score of 11.20 in the SC vaccinated pigs (Group B), from 7-57 with a mean score of 25-80 in the nonvaccinated challenge control pigs (Group C), and 1-28 with a mean score of 10.90 in the non-vaccinated nonchallenged control pigs (Group D). Both IM and SC vaccinated pigs had significantly less lung lesions than the nonvaccinated challenged control pigs (p<0.05). The vaccinated pigs did not have significantly different gross lung lesion scores than the gross lung lesion scores from nonvaccinated nonchallenged pigs (P>0.05). The nonvaccinated challenged control pigs had significantly higher gross lung lesions than the nonvaccinated nonchallenged control pigs (P<0.05).

CONCLUSION

The results of the study demonstrate that Porcine Reproductive and Respiratory Syndrome Virus, Modified Live Virus Vaccine is efficacious for use in healthy pigs three weeks of age or older as an aid in the prevention of respiratory disease caused by virulent PRRSV challenge. One hundred percent of the three week-old pigs vaccinated with the modified live vaccine did not show any adverse local or systemic clinical effects following vaccination. These pigs remained healthy and active for the entire 36 day post vaccination observation period. Pigs vaccinated with a dose of 10^(3.92) TCID₅₀ vaccine either intramuscularly or subcutaneously showed significant reduction (p<0.05) in gross lung lesion development over nonvaccinated challenged control pigs following challenge with a heterologous virulent PRRSV challenge strain, ISU-12. The post challenge gross lung lesion scores of vaccinated pigs were statistically indistinguishable from the nonvaccinated nonchallenged controls (p>0.05). Analysis of the residuals of the parametric analysis of variance indicated that they were distributed normally, substantiating the major assumptions for analysis of variance. One hundred percent of the vaccinated pigs remained free of clinical signs during the post challenge period. TABLE 8 PRRSV Immunogenicity Study: PRRSV Antigen Level of Vaccine* Replicate Titration Number Viral Titer per 2 mL dose 1 10^(3.80) 2 10^(3.93) 3 10^(4.13) 4 10^(3.93) 5 10^(3.80) Average 10^(3.92) *in log TCID₅₀

TABLE 9 PRRSV Immunogenicity Study: PRRSV Gross Lung Lesion Scoring 10 DPC Group C D A B Non Vaccinated Non Vaccinated Pig IM SC Challenged Non Challenged Number Vaccinates Vaccinates Controls Controls 1 21 7 53 4 2 1 12 7 8 3 19 5 57 1 4 12 17 12 2 5 29 3 18 3 6 5 18 35 11 7 18 19 20 24 8 6 5 28 14 9 4 7 32 28 10 0 8 41 14 11 16 3 27 12 12 27 19 13 9 16 40 14 29 19 10 15 17 1 24 16 20 13 15 17 26 12 9 18 21 14 9 19 6 13 35 20 12 5 25 Mean 14.15 11.20 25.80 10.90 Standard 8.86 6.84 14.47 9.3 Deviation

EXAMPLE 7

Complete Sequence of PRRSV Isolate VR 2385

Materials and Methods

Virus and Cells. The PRRSV isolate VR2355, passage 7 was used in this study. A continuous cell line, ATCC CRL 11171 was used for growth of the virus and isolation of viral RNA and total RNA from the virus-infected cell culture.

Cloning of cDNA and PCR amplification. For characterization of the ORF 1 region of genome of VR2385 a random cDNA λ library was constructed using the Uni-Zap cDNA cloning kit (Stratagene, La Jolla, Calif.). Briefly, the CRL11171 cells were infected with VR2385 virus at a M.O.I. of 0.1 and the total RNA from infected cells was isolated at 24 hrs post infection by using a guanidinium thiocyanate method. Initially, probe specific for 5′ end of ORF2 was used to screen the random cDNA library. Plaques that hybridized with the probe were isolated and purified. The phagemids containing viral cDNA inserts were rescued by in vitro excision using ExAssist helper phage and E. coli SOLR cells (Stratagene, LaJolla, Calif.). After hybridizations with ORF1-specific overlapping fragments, several recombinant phagemids with virus specific cDNA inserts with sizes ranging from 2 to 6 kb were selected. The plasmids containing virus cDNA inserts were subsequently purified and sequenced by Sanger's dideoxynucleotide chain termination method with an automated DNA sequencer (Applied Biosystems, Foster City, Calif.). Universal, reverse and PRRSV-specific internal primers were used to determine the sequence. At least 2 independent cDNA clones representing sequence of ORFs 1a and 1b were sequenced. One region, not represented in the library (nt 1950-2050) was PCR amplified with primers 1M687 (5′-CCCCATTGTTGGACCTGTCC-3′) and IM2500(5′-GTCACAACAGGGACCGAGC-3′) using Tag DNA polymerase with addition of the proofreading Tag Extender (Stratagene). The sequencing data were assembled and analyzed using MacVector (International Biotechnologies, Inc., CT) and GeneWorks (IntelliGenetics, CA) computer programs.

Primer extension experiments and RNA sequencing. Primer extension experiments were performed using SureScript Preamplification System for First Strand cDNA Synthesis (Gibco BRL). ³²P-labeled oligonucleotide RNS (5′-CCAAGCTCCCCTGAAGGAGGCTGTCAC-3′) was mixed with 0.5 μg of viral RA of VR2385 in total volume of 12 μl and RNA was denatured for 10 min at 90° C. The sample was adjusted to a total volume 19 μl with first strand cDNA buffer and incubated for 5 min at 42° C. for primer annealing. Super Script II reverse transcriptase was then added to the reaction and the reaction mixture was incubated at 42° C. or 50° C. for min. Samples were analyzed in 40% polyacrylamide gel. Primer extension products were run next to the sequencing reactions of pPR59 clone, containing partial sequence of the leader. Oligonucleotide RNS served as a primer for the sequencing reaction.

Direct sequencing of purified viral RNA was performed using RT RNA Sequencing Kit (USB, Cleveland, Ohio) with γ³²P-labeled oligonucleotide RNS (5′-CCAAGCTCCCCTGAAGGAGGCT GTCAC-3′) and 151Ext (5′-AGCATCCCAGACATGGTTAAAGGGG-3′). Sequencing was performed according to the manufacturer's instructions using 0.5 μg of purified viral RNA per sequencing reaction.

Results

Leader sequence of PRRSV VR2385. Previously, oligo dT and random cDNA libraries of PRRSV VR2385 in λZap vector and here constructed the sequence for portion of ORF1b and complete ORFs-2-7 were determined. The partial leader sequence of VR2385, 161 nucleotides upstream of the ATG start codon of ORF1, was obtained from clone pPR59. It has been shown previously that the leader sequence of LDV is 156 nucleotides, and that the leader sequence of LV (a European isolate of PRRSV) was 221 nucleotides. In order to determine the complete leader sequence of U.S. PRRSV, primer extension experiments were performed. In one experiment cDNA was synthesized using SuperScript II reverese transcriptase at 42° C. and 50° C. In another experiment rTth DNA polymerase in the presence of Mn was used for cDNA synthesis at 60° C. to minimize potential of secondary structures in leader RNA during cDNA synthesis. In all experiments the length of generated cDNA fragments were the same, about 190 nucleotides. In order to detect the complete leader sequence of PRRSV VR2385, direct sequencing of viral RNA was performed. Virion RNA isolated from virus purified through sucrose gradient was used in a direct RNA sequencing reaction. Direct RNA sequencing was performed with a primer complementary to the leader sequence at positions between 10 and 67 nt upstream of the AUG start codon of ORF1a. In addition to the 161 nt leader sequence previously detected by screening of the cDNA library with leader specific probe, an additional 27 nucleotides of the leader sequence were identified. The two nucleotides at the extreme 5′ end of the leader could not be identified due to the strong bands observed in all four lanes in the sequencing gel. The size of the leader determined by direct RNA sequencing correlated with results of the primer extension experiments. To further confirm the data obtained by direct RNA sequencing, RT-PCR was performed with a 16 b.p. primer, corresponding to the extreme 5′ end of the leader, and an antisense primer located 10 nt upstream of the 3′ end of the leader. An expected 180 b.p. PCR fragment was amplified which is in agreement with the results obtained by direct RNA sequencing. Therefore, the putative size of the leader of PRRSV VR2385 was 190 nt, which is smaller than those reported for LV (221 nt), EAV (212 nt) and SHFV (208 nt), but larger than the leader sequence reported for LDV (156 nt). The sequence of the junction region at the 3′ end of the leader was TTTAACC. The ATG start codon of ORF1a is located immediately downstream of this sequence. Similar results were also reported for LV, LDV and SHFV, in which the start codon of ORF1a is also located after the junction sequence. However, the genome of EAV leader junction sequence was reported 13 nt upstream of the start codon of ORF1a. The percentage of nucleotide sequence identity between the leader sequence of VR2385 and those of LV, LDV and SHFV were 55%, 47% and 38%, respectively. Surprisingly, only the last 44 nucleotides at the 3′ end of the leader of VR2385 possess significant homology with the leader sequence of LV (86% identity in this region). Relatively higher homology was also found in this 44 nt region between VR2385 and LDV (64%) and SHFV (63%). No significant homology was found between leader sequences of VR2385 and EAV.

Cloning and sequencing of PRRSV genome. To analyze ORF1 of PRRSV VR 2385, a random primed cDNA library in λZap vector was constructed from total RNA of virus-infected cells. More than twenty overlapping cDNA clones from cDNA library were selected and sequenced (FIG. 23). For most regions, the sequence was determined from at least two independent clones. The region corresponding to nucleotides 1900-2050 was not represented in the cDNA library, and this genomic region was PCR amplified and sequenced. Sequence analysis showed that the genomic RNA of PRRSV (U.S. isolate VR2385), excluding the polyA sequence, is 15100 nucleotides in length.

Functional domains in ORFs 1a/1b and homology with related viruses. The predicted size of ORF1a is 7197 nucleotides. It extends from nucleotides 191 to 7387 (excluding the stop codon TAG) and encodes a 2399 amino acid polyprotein. The leader-genome junction region is similar to that of LV, and the ATG start codon is located immediately after TTTAACC sequence of the leader. Differences were identified when compared the ORF1 sequences of LV and VR2385. ORF 1a in LV is 7188 nucleotides long and encodes 2396 amino acids, which is only 3 amino acids shorter than that of VR2385. Pairwise comparison of nucleotide sequences of VR2385 and LV indicated that the 5′ end of ORF1a is more divergent than the 3′ end. The nucleotide sequence 55% identities between VR2385 and LV is 61% in the 3′ end of ORF 1a, (from nucleotides 3050 to 7387) in the first 1500 nucleotides of ORF 1a 55%, and 46% in a region between nucleotides 1500 to 2500. The most variable region within ORF1a was located between nucleotides 2500 and 3000, where there was no significant homology between VR2385 and LV. The amino acid identity was 49% for region from 1 to 530 aa, 55% for region from 1100 to 2399 amino acids, and no significant homology in the region extending from amino acids 530 to 1100. Comparison of the ORF1a sequences of VR2385 and LDV revealed that there is a 52% homology in first 2000 nucleotides and 55% homology in the last 3800 nucleotides of ORF 1a (corresponding to 3400-7197 nt in VR2385 and 2850-6678 nt in LDV). The region between 2000 to 3400 nt of VR2385 and 2500 to 2850 nt of LDV is highly variable with more than 500 nt deletion in LDV genome. Comparison of the predicted amino acid sequences showed that there is a 36% of homology for the region extended from amino acids 1 to 500, and 39% for the region, that includes the last 1300 amino acids of predicted proteins (1120 to 2353 aa in VR2385 and 940 to 2226 aa in LDV).

Analysis of the predicted protein encoded by ORF1a of VR2385 revealed the presence of two papain-like cysteine protease domains (aa 63-165 and aa 261-347) and one 3C-like serine protease domain (aa 1542-1644), similar to those described for other arteriviruses and coronaviruses. The hydrophilic profiles of ORF1a proteins of VR2385 were similar to those of LV and LDV. The 5′ half of the proteins (first 1100 aa in VR2385) were mostly hydrophilic, the extreme 3′ end (aa 2230-2399 in VR2385) was hydrophilic and the 3′ half of the protein contains 4 hydrophobic regions (1129-1207 aa, 1240-1286 aa, 1478-1643 aa and 1856-2076 regions of VR2385).

The VR2385 ORF1b is 4389 nucleotides long and it extends from nucleotide 7369 to 11757 (excluding stop codon TGA), and encoded a 1463 aa protein. Comparison of the nucleotide and predicted amino acid sequences of VR2385 ORF1b with those of LV, LDV and EAV confirmed that ORF1b is more conserved than ORF1a. Nucleotide and amino acid homology between VR2385 and LV was 64 and 67% in ORF1b and 58 and 53% in ORF1a, respectively. Comparison of the predicted proteins of VR2385 and EAV showed a 36% homology. The predicted ORF1b protein of VR2385 contains a putative polymerase domain (amino acids 373-576), a putative zinc finger domain (amino acid 647-689), and an RNA helicase domain (amino acids 793-1015) similar to those described for LV, LDV, EAV and coronaviruses.

Molecular characterization of ORF1 regions of coronaviruses and arteriviruses showed that the ORF1 polyprotein is expressed through two overlapping ORFs, ORF1a and ORF1b. The expression of ORF1b, which overlaps with ORF1a in −1 frame, takes place through a so-called ribosomal frameshifting mechanism which allows the ribosome to bypass the ORF1a stop codon and translate ORF1b-encoded protein. The frameshift region consists of a “slippery sequence” followed by pseudoknot structure. Analysis of the ORF1a/ORF1b junction region of VR2385 indicated that the potential slippery sequence (5′-UUUAAAC-3′) is located 3 nucleotides upstream of the stop codon of ORF1a and the proposed pseudoknot structure. This region is very conserved in corona- and arteriviruses and the nucleotide sequence homology in this region between VR2385 and LV was 86%.

Comparison of the leader sequences of VR2385 and LV indicated that these two viruses diverged from each other by point mutations and possibly through recombination. The extensive sequence differences in the leader sequences of these two viruses indicated the leader that sequence in PRRSV is not conserved, and is subject to extensive mutational changes. The most conserved region in the leader was the last 44 nucleotides at the 3′ end, where nucleotide sequence acid identity was 86% between VR2385 and LV, and 68% between VR2385 and LDV. The putative leader sequence of VR2385 was 190 nt, which is 31 nt shorter than that of LV, and 35 nt longer than that of LDV. As shown in FIG. 24, there is a 20 nt deletion in the VR2385 leader (located after nucleotide 145) compared to the leader sequence of the LV. Comparison of the leader sequences of VR2385 and LDV indicates that the highest homology score was obtained when a 20 nt gap was introduced into the corresponding region of the leader sequence of LDV (FIG. 24). Similarly, the highest homology score was obtained when a 50 nt gap was introduced into the LDV leader during alignment of the LV and LDV leader sequences. This result suggests that this region of the leader is not critical for virus replication, and deletions may occur in this region of the leader during virus evolution. This observation also could explain the observed differences in the length leader sequences among VR 2385, LV and LDV.

EXAMPLE 8

Characterization of the Leader Sequence and Leader-Body Junction Sites in Subgenomic mRNAs of PRRSV VR 2385

In order to determine the complete leader sequence of PRRSV VR2385, several approaches were utilized including screening of oligo dT cDNA library with leader-specific ³²P-labeled PCR probe, RNA ligation of the viral RNA (RNA circularization) with T4 RNA ligase followed by RT-PCR with ORF7 and leader specific primers, and direct sequencing of the 5′ end of viral RNA (Example 7). First, a 100 b.p. fragment of leader sequence was used as a probe to detect cDNA clones containing the leader sequence from an oligo dT λ library. Eight cDNA clones were analyzed and sequenced, and these clones were found to represent leader sequences of mRNAs 7 (5 clones), 6 (2 clones) and 2 (1 clone). The size of leader sequence varied from 160 to 163 nucleotides in 6 of the 7 clones. In one of the clones which represents mRNA6, the leader specific sequence was 172 nucleotides. It is possible that strong secondary structure within the leader of the virus prevented complete cDNA synthesis of the leader RNA during the construction of the λ Zap library. In a second experiment, the 3′ and 5′ ends of viral RNA were ligated head to tail by using T4 RNA ligase. After phenol chloroform extraction and precipitation, the ligated RNA was subjected to an RT-PCR reaction with primers IM1003 (antisense oligonucleotide, complementary to the 3′ end of the leader sequence) and IM1004 (oligonucleotide, corresponding to a segment of the 3′ non-coding region of the genome, 100 nucleotides upstream of the poly(A) tail). A diffuse band of the PCR products with sizes ranging from 250 to 350 nucleotides was purified from agarose gel, and cloned into the pSK+ vector. Seven independent clones were sequenced. Sequence analysis indicated that the polyA sequence at the 3′ end of the genome and the leader sequence at the 5′ end of the genome were ligated together in all 7 clones, but only 95-96 nucleotides from the 3′ end of the leader sequence were ligated with 3′ end of the viral genome. The sizes of the polyA sequenced clones varied in each clone ranging from 9 to 42 nucleotides, indicating that sequenced clones were independent. The putative full-length leader sequence of VR2385 was determined by direct RNA sequencing of the 5′-end of virion RNA isolated from sucrose gradient purified virus (Example 7).

Leader mRNA junction sequences and intergenic regions within the genome of VR2385. In order to characterize leader body junction regions of sg RNAs of the VR2385 strain, RT-PCR was performed with leader specific primer and primers, specific for each sg mRNA. Total RNAs isolated at 20 hours post infection (h.p.i.) were used for RT-PCR. The predominant bands were isolated from agarose gel, cloned and sequenced. Direct sequencing of the PCR products was also performed. In order to identify leader body junction region in the genome of the PRRSV, a leader specific ³²P-labeled probe was used to screen a random cDNA library generated from viral RNA, and several clones containing leader-ORF1a junction regions were isolated and sequenced. The leader body junction regions of sg mRNAs 2 to 7 were characterized.

Table 10 summarizes the leader-body junction regions of all sg mRNAs and their corresponding regions in the virus genome. Only a single junction site was detected for sg mRNAs 2,3, and 6, whereas two sites were detected for sg mRNAs 4, 5 and 7, designated as 4a, 4b, 5a, 5b and 7a, 7b. The leader genome junction region in VR2385 was represented by a sequence CCACCCCTTTAACC, which is similar to that of TABLE 10 Sequence of the leader-body junction regions of subgenomic mRNAs of VR2385 RNA SEQUENCE N of clones 5′-leader CCACCCCTTTAACC 4 mRNA2 CCACCCCttgaacc 3 genome cctgtcattgaacc mRNA3 CCACCCCtgtaacc 2 CCACCCCTTtaacc 1 genome ggtcaaatgtaacc mRNA4a CCACCCCTttgacc 1 genome aaggccacttgacc mRNA4b CCACCCCtttcacc 2 CCACCCCgtttcacc 1 genome caattggtttcacc mRNA5.a CCACCCcgtcaact 1 genome agtgtgcgtcaact mRNA5.b CCACCCCtttagcc 2 CCACCCCttttagcc 1 genome caactgttttagcc mRNA6 CCACCCCTgtaacc 3 CCACCCCTTtaacc 1 genome ctacccctgtaacc mRNA7.a CCACCCCTTtaacc 5 CCACCCCTataacc 1 genome ggcaaatgataacc mRNA7.b CCACCCCCTtaaacc 1 genome agggagtggtaaacc

The leader body mRNAs junction regions varied in sg mRNAs 3, 4, 5b, 6 and 7a. Table 11 compares the intergenic regions in genomes of VR2385, LV, LDV and EAV. The intergenic regions of VR2385, LV and LDV are very similar. Most variations were found in the first three nucleotides of these regions, whereas the last four nucleotides are conserved and in most regions are represented by the sequence AACC. Variations were also found in the first two nucleotides of this junction sequence (GACC and CACC in the intergenic region of ORF4 of VR2385, AGCC in the intergenic region of ORF5b of VR2385, GACC in the intergenic region of ORF3 in LV, and ACC in the intergenic region of ORF2 of LDV). The intergenic region for sg mRNA5a of VR2385 is GUCAACU, which is similar to that of EAV. TABLE 11 Sequence of the 3′ end of the leader in the genome (RNA1) and junction sites of subgenotnic mRNAs 2 to 7 of VR2385, LV, LDV and EAV. RNA VR2385 LV LDV EAV 1 UUUAACC UUUAACC UAUAACC AUCAACU 2 UUGAACC GUAAACC UAU-ACC UUCAACU 3.1 UGUAACC GUUGACC UGUAACC GUCAA-U 3.2 AUCAACU 3.3 AU-AAUU 4a CUUGACC 4b UUUCACC UUCAACC UGUAACC GUCAACU 5.a GUCAACU 5.b UUUAGCC UACAACC UAUAACC GUCAACU 6 UAUAACC CUCAACC UAAAACC GUCAACC 7.a GAUAACC 7.b GUAAACC GUUAACC CCUAACC CUCAACU

The positions of intergenic sites upstream of the start codon of the corresponding ORFs vary from 4 to 231 nucleotides. Table 12 compares the location of intergenic sites in the genomes of VR2385 and LV (numbers represents distance in nucleotides between the intergenic site and AUG start codon of the corresponding ORF.) The locations of these sites in the genome of VR2385 and LV differ in sg mRNAs 3, 4, 5 and 6. Three alternative intergenic sites for the synthesis of sg mRNAs 4,5 and 7 of VR2385 genome were also identified. Previously, that only six bands of sg mRNAs were detected in the cells infected with VR2385 by Northern blot hybridization analysis. To confirm that the additional sg mRNAs are actually synthesized during the replication of VR2385, a nested RT-PCR was performed by using leader and ORF specific primers. The amplified PCR products were similar in sizes corresponding to additional mRNAs 4a 5a and 7a (FIG. 26). The results indicated that the intergenic sites 4b and 5b of sg mRNAs 4 and 5 which is located closer to the start codon of the corresponding ORF were frequently used in sg mRNA synthesis. The sg mRNAs 4 and 5 were predominantly generated from intergenic sites 4b and 5b while only a minor population was generated by using alternative sites 4a and 5a. In the case of sg mRNA7 the integenic site 7a located 123 nt upstream of start codon of ORF7 was frequently used, whereas site 7b located 9 nt upstream of start codon of ORF7 was less involved in sg mRNA7 synthesis. TABLE 12 Location of the intergenic sites inside of the genome of VR2385 and LV. Position of the junction site RNA VR2385 LV RNA2 20 38 RNA3 83 11 RNA4 231 & 4 83 RNA5  157 & 40 32 RNA6 17 24 RNA7 123 & 9 9

Comparison of the leader genome junction sequence with sequences of the intergenic regions and sequences of leader body junction regions in sg mRNAs indicated that only the last seven nucleotides of leader (TTTAACC) possess homology with the sequences of the intergenic regions in the genome of VR2385. The overall homology varies from 5 to 7 nt, and the only exception was sg mRNA6 where 11 out of 12 nt in the intergenic region are similar to the 3′ end of the leader sequence. In the leader body junction regions of the sg mRNA, the CCACCCC sequence is conserved and generated from leader. The sequence following CCACCCC, however, varied for different sg mRNAs, but has a high level of homology with the TTTAACC sequence at the 3′ end of the leader. The variations in the leader body junction sequences detected for different sg mRNAs indicates that leader body joining is imprecise. Nucleotide sequence comparisons between the 3′ end of the leader, leader body junction regions of the sg mRNAs and intergenic regions within the genome of VR2385 allowed detection of regions of actual joining between leader and body of sg mRNA (Table II, underlined).

Conclusions. The mechanism of subgenomic mRNA synthesis of U.S. isolates of PRRSV is similar to that of LV, LDV and EAV. Intergenic regions detected in VR2385 were more variable and were located at different sites when compared to LV. Variations in leader body junction sequences indicate that leader body joining is imprecise. The locations of actual leader body joining sites in sg mRNAs suggest that mechanism(s) other than leader priming may be involved in the synthesis of sg mRNAs. Alternative leader-body junction sites in the genomes of U.S. isolates of PRRSV can result in the variation of the number of sg mRNA among different strains of PRRSV.

EXAMPLE 9

The following provides a reliable test for the identification and differentiation of high passage ISU55 strain of PRRSV from field isolates of PRRSV. In previous studies the sequence of the low passage ISU55 strain (passage 7) was determined and this sequence was used to develop an RFLP test for differentiation of ISU55 hp strain. As a first step, the sequence of ISU55 p-7 was analyzed to identify variable regions containing unique restriction sites. After computer sequence analysis and comparison with sequences of different PRRSV strains, a specific region containing two unique restriction sites was identified at the 3′ end of ORF4. These two restriction sites were DraI (TTT/AAA) at position 1510 and BalI (MscI) (TGG/CCA) at position 1697 relative to the location upstream of the ATG start codon of ORF2 in ISU55 (p-7) sequence. These two restriction sites were present only in the corresponding region of ISU55 strain but not in the other PRRSV strains.

In order to confirm the results of the computer analysis, the sequence of high passage ISU55 strain was determined. The genomic region including ORFs 3 to 7 (2696 b.p.) was amplified by PCR and sequenced. The sequence of high passage ISU55 was compared with that of the ISU55 passage 7. The results of this comparison are shown in FIG. 27 (cDNA alignment), FIG. 28 (ORF maps) and FIG. 29 (restriction pattern with restriction enzymes DraI and BalI). The sequences of the low passage and high passage of PRRSV ISU55 were very conserved. There were only 15 nucleotide substitutions in high passage ISU55 strain. The sizes and relative positions of ORFs 3 to 7 remain the same. A single nucleotide change in the high passage virus created an additional DraI site in the sequence of the high passage virus compared to the low passage ISU55 (FIG. 29). This finding affords an opportunity to distinguish the high passage virus from the low passage ISU55 virus. A BLAST search was conducted to compare specific regions of ISU55 high passage strain with other PRRSV sequences available in the GenBank database. The 237b.p. fragment including the unique restriction sites of ISU 55 high passage strain (two DraI sites at position 966 and 1159 and BalI site at position 1157, restriction map of ISU55 hp.) was used as the template for comparison. The results of the blast search indicated that these sites are unique for ISU55 high passage strain and are not present in 24 other PRRSV isolates available in the database.

The ORF5 (603 bp.) of ISU55 high passage strain was also compared with the ORF5 of other PRRSV strains. As expected, ISU55 passage 7 strain has the highest homology score and there are only 3 nucleotide substitutions. The strain with the second highest homology score was NADC8 which has 33 nucleotide substitutions in ORF5 compared to the ORF5 of ISU55 hp strain. The rest of PRRSV strains compared in the BLAST search displayed more variations (up to 63 nt changes) in the ORF5. These data clearly indicate that ISU55 PRRSV strain is different from all other PRRSV strains characterized so far.

An PCR-RFLP was developed to differentiate ISU55 high passage strain from ISU55 lp virus and other strains of PRRSV. For the RFLP test two primers were synthesized: forward primer 55F 5′-CGTACGGCGATAGGGACACC-3′ (pos. 823) and reverse primer 3RFLP 5′-GGCATATATCATCACTGGCG-3′ (pos. 1838) (positions from the 5′ end of 2696 bp. sequenced fragment of ISU55 high passage strain). The reverse primer for the PCR-RFLP test was the same as the one used in a PCR-RFLP test to differentiate MLV ResPRRSV vaccine strain since this primer has been used in the PCR-RFLP with a large number of PRRSV isolates and shown to be specific (Wesley et al, J. Vet. Diagn. Invest. 10:140-144 (1998); Wesley et al, Amer. Assoc. Of Swine Practitioners, pp. 141-143 (1996); Andreyev et al, Arch. Virol. 142:993-1001 (1997); Mengeling, et al, 1997, all of which are incorporated herein by reference in their entireties). These two primers amplify a 1026 bp cDNA fragment of PRRSV ISU55 high passage strain. After digestion with restriction enzyme with DraI three fragments (626 bp, 187 bp and 135 bp) will be generated. After digestion with BalI, two fragments with sizes 626 and 322 bp will be formed. After PCR and restriction enzyme digestions of other PRRSV strains, a 1026 bp fragment will be formed according to the analysis of computer data. To validate the PCR-RFLP test, total RNA was isolated from ISU55 hp, ISU12 lp, ISU12 hp strains and subjected to RT-PCR with primers 55F and 3RFLP. A 1026 bp fragment was amplified from all the isolates. These fragments were purified and digested with restriction enzymes DraI and BalI. The resulting products were analyzed in 1.5% agarose gel. FIG. 30 shows the results of the test. Line one shows an untreated 1026 bp PCR fragment of ISU55hp strain. Line 2 and 5 shows PCR products of ISU55 hp digested with DraI (line 2) and BalI (line 5). The 626 bp, 187 bp and 135 bp fragments were formed after digestion with DraI, and 626 and 322 bp. fragments were formed after digestion with BalI. Lines 3, 4, 6, and 7 show results of DraI digestion (lines 3 and 4) and BalI digestion (lines 6 and 7) of PCR products of ISU12 lp (lines 3 and 6) and ISU12 hp (lines 4 and 7) strains. In all reactions with ISU12 lp and hp strains a PCR fragment of 1026 bp was detected. These data correlate with the predictions for the PCR-RFLP differentiation test for the ISU55 hp strain.

Obviously, numerous modifications and variations of the present invention are possible in light of the above teachings. It is therefore to be understood that within the scope of the appended claims, the invention may be practiced otherwise than as specifically described herein.

EXAMPLE 10

Sequencing of the Genome of the Attenuated PRRSV Vaccine Strain (ISU55 p49).

After the sequence of VR2385 strain was determined, generated sequencing information was used in order to determine sequence of the attenuated vaccine PRRSV strain (Vaccine Strain). The entire genome of Vaccine Strain was amplified in 21 overlapping fragments and sequenced. When sequencing data were combined, the entire size of the gnome was 15,412 nucleotides, which is 309 nt longer compare to the length of the genome of VR2385 strain. The ORFs map and their locations are shown on FIG. 31. Genome comparison of Vaccine Strain and VR2385 strains showed the same sizes and relative locations of the ORFs lb through ORF7. The ORF1a was the most variable and one 309 nucleotides deletion was found in the genome of VR2385 compared to the sequence of Vaccine Strain. This deletion was in frame and located in the region of ORF1a at position 3242 nucleotide from the 5′ end of genome of VR2385 PRRSV. Another three nucleotides were deleted in the region 2504-2515 nt of the genome causing 1 aa deletion compare to the genome of Vaccine Strain. Results of genome comparison of different ORFs of Vaccine Strain and VR2385 strain are summarized in the Table 13. Overall DNA homology between these strains was about 91% with 14094 nucleotides identical in both strains. Not including 309 nt deletion DNA homology was 93%. Leader sequence was determined only for VR2385 strain by direct sequencing of the viral RNA and 17 bp primer specific for 5′ end of the leader of VR2385 was used to amplify 170 nt portion of the leader of Vaccine Strain. Comparison of these sequences showed overall homology of 94% with single nucleotides deletions in both strains: nucleotides A (pos. 75) and G (pos. 119) of VR2385 leader are missing in the leader of Vaccine Strain, and nucleotides A (pos. 87) and G (pos. 124) of Vaccine Strain leader are missing in the leader of VR2385 strain.

The ORF1a in the Vaccine Strain extends from nts 191 to 7699 and encodes 2503 amino acid (aa) protein, which is 103 aa longer compare to the ORF 1a protein of VR2385 strain. Overall aa identity in between ORF1a predicted proteins of the Vaccine Strain and VR2385 was 88% (92% not including deletion in VR2385). Comparison with ORF1a protein of LV showed approximately 47% of aa identity overall, but several regions with different protein similarity can be identified. Relatively conservative 5′ end (aa 1 to 529 in Vaccine Strain and aa 1 to 521 in LV, 50% aa identity), relatively conservative 3′ end (aa 1232 to 2503 in Vaccine Strain and aa 1115 to 2396 in LV, 58% aa identity), and hypervariable region (HVR) in between (aa 530 to 1231 in Vaccine Strain and aa 522 to 1114 in LV, aa identity less than 40%). When we studied homology in HVR in more details, we were able to detect one short region (94 aa), where aa homology was 50% between Vaccine Strain and LV. This region extends from aa 1015 to 1108 in the Vaccine Strain and aa 929 to 1021 in LV. Interestingly, in exception of the first four aa (ITRK) this region was deleted in VR2385 strain. To summarize, homology in the ORF 1a predicted protein can be presented as follows: conservative region 1 (aa 1 to 529 in the vaccine Strain/VR2385 strain, aa 1 to 521 in LV, 90% a identity between Vaccine Strain and VR2385, 50% aa identity between Vaccine/VR2385 strains and LV), hypervariable region (HVR) (aa 530 to 1231 in the Vaccine Strain, aa 520 to 1127 in the VR2385 strain, aa 522 to 1232 in LV, 84% aa identity between Vaccine Strain and VR2385, 103 aa deletion in the ORF 1a protein of VR2385, less then 40% aa identity between Vaccine/VR2385 strains and LV), and conservative region 2 (aa 1232 to 2503 in the Vaccine Strain, aa 1128 to 2399 in the VR2385 strain, aa 1128 to 2396 in LV, 96% aa identity between Vaccine Strain and 57% aa identity between Vaccine/VR2385 strains and LV). The 94 amino acid fragment (aa 929 to 1021) in the HVR of the Vaccine Strain posses 50% aa homology with LV, and this region is deleted in VR2385 strain.

The ORF 1b in the Vaccine Strain extends from nts 7687 to 12069 and encodes 1461 aa protein, which is similar in size to that of VR2385. Nucleotide and amino acid comparison showed, that ORF1b is much more conservative compare to ORF1a. Nucleotide homology between Vaccine Strain and VR2388 was 93%, with 97% homology of their predicted proteins. Comparison with ORF1b of LV (1462 aa) showed 67% of aa identity. One variable region was detected at the 3′ end of ORF1b (aa 1367-1461) compare to LV.

The ORF2 to ORF7 region of the vaccine strain showed similar genome organization to that of VR2385, with similar sizes and relative locations of the ORFs. Data of homology comparison between Vaccine Strain and VR2385 are presented in the Table 13, Nucleotide (amino acid) identity of Vaccine Strain with LV was 66% (61%) for ORF2, 61% (55%) for ORF3, 66% (67%) for ORF4, 63% (51%) for ORF5, 68% (79%) for ORF6, and 60% (58%) for ORF7. TABLE 13 Comparison of the ORFs and DNA homology between VR2385 p8, ISU55 p49 (Vaccine Strain) and LV Size of the ORF Homology with (nucleotides) VR2385:nt(aa) ORF VR2385 ISU55 LV ISU55 LV 1a 7197 7509 7188 89 (88) 1b 4383 4383 4386 93 (97) 64 (67) 2 768 768 747 97 (95) 65 (60) 3 762 762 795 94 (95) 64 (55) 4 534 534 549 96 (97) 66 (66) 5 600 600 603 93 (90) 63 (54) 6 522 522 519 97 (93) 68 (78) 7 369 369 384 96 (94) 60 (57)

EXAMPLE 11

Analysis of Deletions in VR 2385 Isolates.

A PCR product amplified from VR 2385 PRRSV showed the presence of a 445 bp deletion in the ORF1a. The 445 bp deletion, as well as the 309 bp deletion noted above, were in frame, overlapped and appeared to of independent origin. It was assumed that after plaque purification these deletion variants appeared in the population of VR2385 and the variant with the 445 nt deletion became predominant in the virus stock. This variant appears to be stable based on PCR studies of RNA isolated from low passage virus, high passage virus and from virus passed twice through pig. The 309 bp deletion variant appeared to be minor and could be amplified from some virus stocks with specific primers only by nested PCR.

EXAMPLE 12

Characterization of Serially Passaged PRRSV.

To determine if attenuation occurs due to cell culture passage, VR 2385 passage 7 (p7) and VR 2385 passage 85 (p85) were used to infect 3 week-old pigs. At 10 days post-infection, estimated gross lung lesions and clinical respiratory scores were significantly higher in the pigs infected with the lower passage virus. The ORF 2-7 region of the genome was sequenced and compared. Genetic analysis of the two passages of VR 2385 shows that ORF 6 was the most conserved, with 100% homology at the amino acid level. The remaining ORFs showed amino acid homology of 95-98%, with ORF2 of VR 2385 p85 containing a premature stop codon resulting in a putative 10 amino acid truncation. 

1. A DNA sequence encoding a porcine reproductive and respiratory syndrome virus (PRRSV) consisting of SEQ ID NO:______ (ISU-12).
 2. A DNA sequence encoding an open reading frame of the PRRSV of claim 1 selected from the group consisting of nucleotides 191-7387 of SEQ ID NO:______ (ORF1a), nucleotides 7375-11757 of SEQ ID NO:______ (ORF 1b), nucleotides 11762-12529 of SEQ ID NO:______ (ORF 2), nucleotides 12385-13116 of SEQ ID NO:______ (ORF 3), nucleotides 12930-13463 of SEQ ID NO:______ (ORF 4), nucleotides 13477-14076 of SEQ ID NO:______ (ORF 5), nucleotides 14064-14585 of SEQ ID NO:______ (ORF 6) and nucleotides 14578-14946 of SEQ ID NO:______ (ORF 7).
 3. A polypeptide encoded by the DNA sequence of claim
 2. 4. A composition for inducing antibodies against PRRSV comprising one or more polypeptides encoded by the DNA sequences of claim
 2. 5. A DNA sequence encoding a PRRSV consisting of SEQ ID NO:______ (ISU-55).
 6. A DNA sequence encoding an open reading frame of the PRRSV of claim 5 selected from the group consisting of nucleotides 191-7699 of SEQ ID NO:______ (ORF1a), nucleotides 7687-12069 of SEQ ID NO:______ (ORF 1b), nucleotides 12074-12841 of SEQ ID NO:______ (ORF 2), nucleotides 12692-13458 of SEQ ID NO:______ (ORF 3), nucleotides 13212-13775 of SEQ ID NO:______ (ORF 4), nucleotides 13789-14388 of SEQ ID NO:______ (ORF 5), nucleotides 14376-14592 of SEQ ID NO:______ (ORF 6) and nucleotides 14890-15258 of SEQ ID NO:______ (ORF 7).
 7. A polypeptide encoded by the DNA sequence of claim
 6. 8. A composition for inducing antibodies against PRRSV comprising an amount of a PRRSV encoded by SEQ ID NO:______ (ISU-55) effective to induce said antibodies in a pig, and a physiologically acceptable carrier.
 9. A composition for inducing antibodies against PRRSV comprising one or more polypeptides encoded by the DNA sequences of claim
 6. 10. The composition of claim 8, wherein lung lesions in said five-week-old colostrum-deprived, caesarean-derived pigs are reduced by a statistically significant amount wherein said amount is significant a p value less than 0.01, relative to lung lesions in uninoculated five-week-old colostrum-deprived, caesarean-derived pigs.
 11. The composition of claim 9, wherein lung lesions in said five-week-old colostrum-deprived, caesarean-derived pigs are reduced by a statistically significant amount wherein said amount is significant a p value less than 0.101, relative to lung lesions in uninoculated five-week-old colostrum-deprived, caesarean-derived pigs.
 12. The composition of claim 8 further comprising an adjuvant.
 13. The composition of claim 9 further comprising an adjuvant.
 14. A method of protecting a pig from a porcine reproductive and respiratory disease, comprising administering an effective amount of the composition of claim 8 to a pig in need of protection against said disease.
 15. The method of claim 14, wherein said vaccine is administered orally or parenterally.
 16. The method of claim 14, wherein said vaccine is administered intramuscularly, intradermally, intravenously, intraperioneally, subcutaneously or intranasally.
 17. A method of protecting a pig from a porcine reproductive and respiratory disease, comprising administering an effective amount of the composition of claim 9 to a pig in need of protection against said disease.
 18. The method of claim 17, wherein said vaccine is administered orally or parenterally.
 19. The method of claim 17, wherein said vaccine is administered intramuscularly, intradermally, intravenously, intraperitoneally, subcutaneously or intranasally.
 20. A method of distinguishing PRRSV strain ISU-55 from other strains of PRRSV comprising: (a) amplifying a DNA sequence of the PRRSV using the following two primers: 55F 5′-CGTACGGCGATAGGGACACC-3′ and 3RFLP 5′-GGCATATATCATCACTGGCG-3′;

(b) digesting the amplified sequence of step (a) with DraI; and (c) correlating the presence of three restriction fragments of 626 bp, 187 bp and 135 bp with a PRRSV ISU-55 strain. 